Fix for #248

scripts/java/application.yaml

@@ -1,10 +1,11 @@
 ontology:
-  directory: ../../owl/
-  to-collapse:
+  directory: ../../owl/ # where to load the ontologies from
+  format: rdf_xml # which format to use (optional - if not given, the default format will be used). Possible Values: xml, owl_xml, functional, manchester (the latter is not recommended because GCIs will get lost). Parameter is not case sensitive.
+  to-collapse: # which ontologies to collapse
     - ontology: SOMA-All
       out-path: ../../build/owl/current/SOMA.owl
-      except: DUL
-      new-iri: https://ease-crc.github.io/soma/owl/current/SOMA.owl
+      except: DUL # Optional, which ontologies should not be merged but still be imported
+      new-iri: https://ease-crc.github.io/soma/owl/current/SOMA.owl # Optional, if the IRI of the collapsed version should be different from the original
     - ontology: SOMA-HOME
       out-path: ../../build/owl/current/SOMA-HOME.owl
       except: DUL

scripts/java/src/main/java/main/Application.java

@@ -1,11 +1,13 @@
 package main;
 
+import main.config.CollapseConfig;
+import main.config.OntologyConfig;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 
 @SpringBootApplication
-@EnableConfigurationProperties({CollapseConfig.class,OntologyConfig.class})
+@EnableConfigurationProperties({CollapseConfig.class, OntologyConfig.class})
 public class Application {
 
 	public static void main(final String... args) {

scripts/java/src/main/java/main/CIRunner.java

@@ -0,0 +1,32 @@
+package main;
+
+import main.ci_runners.*;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.stereotype.Component;
+
+@Component
+public class CIRunner implements CommandLineRunner {
+
+	@Autowired
+	private Collapser collapser;
+
+	@Autowired
+	private IsDefinedInAdder isDefinedInAdder;
+
+	@Autowired
+	private VersionInfoAdder versionInfoAdder;
+
+	@Autowired
+	private OntologySaver ontologySaver;
+
+
+	@Override
+	public void run(final String... args) throws Exception {
+		final CIRunnable[] toRun = {isDefinedInAdder, versionInfoAdder, collapser, ontologySaver};
+		for (final var next : toRun) {
+			next.run();
+		}
+	}
+
+}

scripts/java/src/main/java/main/OntologyManager.java

@@ -1,5 +1,6 @@
 package main;
 
+import main.config.OntologyConfig;
 import org.protege.xmlcatalog.owlapi.XMLCatalogIRIMapper;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;

scripts/java/src/main/java/main/ci_runners/CIRunnable.java

@@ -0,0 +1,6 @@
+package main.ci_runners;
+
+public interface CIRunnable {
+
+	void run() throws Exception;
+}

scripts/java/src/main/java/main/Collapser.java → scripts/java/src/main/java/main/ci_runners/Collapser.java

@@ -1,25 +1,25 @@
-package main;
+package main.ci_runners;
 
+import main.OntologyManager;
+import main.config.CollapseConfig;
+import main.config.OntologyConfig;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.model.parameters.Imports;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.CommandLineRunner;
 import org.springframework.stereotype.Component;
 import org.springframework.util.CollectionUtils;
 
-import javax.annotation.Priority;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Optional;
 import java.util.function.Supplier;
 
 @Component
-@Priority(Integer.MAX_VALUE - 1)
-public class Collapser implements CommandLineRunner {
+public class Collapser implements CIRunnable {
 
 	/**
 	 * {@link Logger} of this class.
@@ -40,8 +40,7 @@ public Collapser(final OntologyManager ontologyManager, final OntologyConfig ont
 	}
 
 	@Override
-	public void run(final String... args)
-			throws OWLOntologyStorageException, OWLOntologyCreationException, IOException {
+	public void run() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
 		for (final var collapseConfig : ontologyConfig.toCollapse()) {
 			collapse(collapseConfig);
 		}

scripts/java/src/main/java/main/IsDefinedInAdder.java → scripts/java/src/main/java/main/ci_runners/IsDefinedInAdder.java

@@ -1,5 +1,6 @@
-package main;
+package main.ci_runners;
 
+import main.OntologyManager;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.AxiomType;
 import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
@@ -9,16 +10,13 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.CommandLineRunner;
 import org.springframework.stereotype.Component;
 
-import javax.annotation.Priority;
 import java.util.Collection;
 import java.util.HashSet;
 
 @Component
-@Priority(0)
-public class IsDefinedInAdder implements CommandLineRunner {
+public class IsDefinedInAdder implements CIRunnable {
 
 	/**
 	 * {@link Logger} of this class.
@@ -34,7 +32,7 @@ public IsDefinedInAdder(final OntologyManager ontologyManager) {
 
 
 	@Override
-	public void run(final String... args) {
+	public void run() {
 		for (final OWLOntology ontology : ontologyManager.getOntologyManager().getOntologies()) {
 			addIsDefinedIn(ontology);
 		}

scripts/java/src/main/java/main/OntologySaver.java → scripts/java/src/main/java/main/ci_runners/OntologySaver.java

@@ -1,36 +1,40 @@
-package main;
+package main.ci_runners;
 
+import main.OntologyManager;
+import main.config.OntologyConfig;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.CommandLineRunner;
 import org.springframework.stereotype.Component;
 
-import javax.annotation.Priority;
-
 @Component
-@Priority(Integer.MAX_VALUE - 1)
-public class OntologySaver implements CommandLineRunner {
+public class OntologySaver implements CIRunnable {
 
 	/**
 	 * {@link Logger} of this class.
 	 */
 	private static final Logger LOGGER = LoggerFactory.getLogger(OntologySaver.class);
 	private final OntologyManager ontologyManager;
+	private final OntologyConfig ontologyConfig;
 
 	@Autowired
-	public OntologySaver(final OntologyManager ontologyManager) {
+	public OntologySaver(final OntologyManager ontologyManager, final OntologyConfig ontologyConfig) {
 		this.ontologyManager = ontologyManager;
+		this.ontologyConfig = ontologyConfig;
 	}
 
 	@Override
-	public void run(final String... args) throws OWLOntologyStorageException {
+	public void run() throws OWLOntologyStorageException {
 		for (final OWLOntology ontology : ontologyManager.getOntologyManager().getOntologies()) {
 			LOGGER.info("Saving {}", ontology.getOntologyID().getOntologyIRI().map(Object::toString)
 			                                 .orElseGet(() -> "unnamed ontology"));
-			ontology.saveOntology();
+			if (ontologyConfig.format() == null) {
+				ontology.saveOntology();
+			} else {
+				ontology.saveOntology(ontologyConfig.format());
+			}
 		}
 	}
 }

scripts/java/src/main/java/main/ci_runners/VersionInfoAdder.java

@@ -0,0 +1,51 @@
+package main.ci_runners;
+
+import main.OntologyManager;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.AddOntologyAnnotation;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+@Component
+public class VersionInfoAdder implements CIRunnable {
+
+
+	/**
+	 * {@link Logger} of this class.
+	 */
+	private static final Logger LOGGER = LoggerFactory.getLogger(VersionInfoAdder.class);
+
+	private final OntologyManager ontologyManager;
+
+
+	private final String versionInfo;
+
+	@Autowired
+	public VersionInfoAdder(final OntologyManager ontologyManager, @Value("${versionInfo}") final String versionInfo) {
+		this.ontologyManager = ontologyManager;
+		this.versionInfo = versionInfo;
+	}
+
+
+	@Override
+	public void run() {
+		for (final OWLOntology ontology : ontologyManager.getOntologyManager().getOntologies()) {
+			addVersionInfo(ontology, versionInfo);
+		}
+	}
+
+	private static void addVersionInfo(final OWLOntology ontology, final String version) {
+
+		final var df = OWLManager.getOWLDataFactory();
+		final var versionAnnotation = df.getOWLAnnotation(df.getOWLVersionInfo(), df.getOWLLiteral(version));
+		ontology.getOWLOntologyManager().applyChange(new AddOntologyAnnotation(ontology, versionAnnotation));
+
+		LOGGER.info("Added versionInfo {} to {}", version, ontology.getOntologyID().getOntologyIRI());
+	}
+
+
+}

scripts/java/src/main/java/main/CollapseConfig.java → scripts/java/src/main/java/main/config/CollapseConfig.java

@@ -1,4 +1,4 @@
-package main;
+package main.config;
 
 import org.semanticweb.owlapi.model.HasOntologyID;
 import org.semanticweb.owlapi.model.IRI;

scripts/java/src/main/java/main/OntologyConfig.java → scripts/java/src/main/java/main/config/OntologyConfig.java

@@ -1,12 +1,13 @@
-package main;
+package main.config;
 
+import org.semanticweb.owlapi.model.OWLDocumentFormat;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 
 import java.nio.file.Path;
 import java.util.Collection;
 
 
 @ConfigurationProperties(prefix = "ontology")
-public record OntologyConfig(Path directory, Collection<CollapseConfig> toCollapse) {
+public record OntologyConfig(Path directory, Collection<CollapseConfig> toCollapse, OWLDocumentFormat format) {
 
 }

scripts/java/src/main/java/main/IRIConverter.java → scripts/java/src/main/java/main/converter/IRIConverter.java

@@ -1,4 +1,4 @@
-package main;
+package main.converter;
 
 import org.jetbrains.annotations.NotNull;
 import org.semanticweb.owlapi.model.IRI;

scripts/java/src/main/java/main/converter/OWLDocumentFormatConverter.java

@@ -0,0 +1,26 @@
+package main.converter;
+
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
+import org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat;
+import org.semanticweb.owlapi.formats.OWLXMLDocumentFormat;
+import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
+import org.semanticweb.owlapi.model.OWLDocumentFormat;
+import org.springframework.boot.context.properties.ConfigurationPropertiesBinding;
+import org.springframework.core.convert.converter.Converter;
+import org.springframework.stereotype.Component;
+
+@Component
+@ConfigurationPropertiesBinding
+public class OWLDocumentFormatConverter implements Converter<String, OWLDocumentFormat> {
+
+	@Override
+	public OWLDocumentFormat convert(final String source) {
+		return switch (source.toUpperCase()) {
+			case "RDF_XML" -> new RDFXMLDocumentFormat();
+			case "OWL_XML" -> new OWLXMLDocumentFormat();
+			case "FUNCTIONAL" -> new FunctionalSyntaxDocumentFormat();
+			case "MANCHESTER" -> new ManchesterSyntaxDocumentFormat();
+			default -> throw new IllegalStateException("Unexpected value: " + source);
+		};
+	}
+}