guess versionname from versionIRI metadata (862907e9) · Commits · SAREF / saref-pipeline

src/main/java/fr/emse/gitlab/saref/SAREF.java

+32 −0

Original line number	Original line	Diff line number	Diff line
	@@ -25,14 +25,24 @@
	*/		*/
	package fr.emse.gitlab.saref;		package fr.emse.gitlab.saref;

			import java.io.File;
			import java.io.FileInputStream;
			import java.io.InputStreamReader;
			import java.nio.charset.Charset;
			import java.nio.charset.MalformedInputException;
	import java.nio.file.FileSystems;		import java.nio.file.FileSystems;
	import java.nio.file.PathMatcher;		import java.nio.file.PathMatcher;
	import java.util.ResourceBundle;		import java.util.ResourceBundle;
	import java.util.regex.Matcher;		import java.util.regex.Matcher;
	import java.util.regex.Pattern;		import java.util.regex.Pattern;

			import org.apache.jena.atlas.RuntimeIOException;
			import org.apache.jena.riot.Lang;
			import org.slf4j.Logger;

	import fr.emse.gitlab.saref.entities.SAREFCore;		import fr.emse.gitlab.saref.entities.SAREFCore;
	import fr.emse.gitlab.saref.entities.SAREFExtension;		import fr.emse.gitlab.saref.entities.SAREFExtension;
			import fr.emse.gitlab.saref.entities.SAREFNamedGraph;
	import fr.emse.gitlab.saref.entities.SAREFProject;		import fr.emse.gitlab.saref.entities.SAREFProject;
	import fr.emse.gitlab.saref.entities.SAREFVersionName;		import fr.emse.gitlab.saref.entities.SAREFVersionName;

	@@ -143,4 +153,26 @@ public class SAREF {
	}		}
	return msg;		return msg;
	}		}


			public static void loadModel(SAREFNamedGraph namedGraph, File file, Logger logger) {
			try (FileInputStream input = new FileInputStream(file)) {
			namedGraph.getModel().read(input, SAREF.BASE, Lang.TTL.getLabel());
			} catch (Exception ex) {
			if (ex instanceof RuntimeIOException && ex.getCause() instanceof MalformedInputException) {
			namedGraph.getModel().removeAll();
			try (InputStreamReader input2 = new InputStreamReader(new FileInputStream(file),
			Charset.defaultCharset())) {
			namedGraph.getModel().read(input2, SAREF.BASE, Lang.TTL.getLabel());
			} catch (Exception ex2) {
			namedGraph.getModel().removeAll();
			String msg = getMessage("turtle", namedGraph.getIRI());
			logger.error(msg, ex2);
			}
			} else {
			String msg = getMessage("turtle", namedGraph.getIRI());
			logger.error(msg, ex);
			}
			}
			}
	}		}

src/main/java/fr/emse/gitlab/saref/managers/OntologyManager.java

+4 −0

Original line number	Original line	Diff line number	Diff line
	@@ -29,6 +29,9 @@ import java.io.IOException;
	import java.util.Set;		import java.util.Set;
	import java.util.function.Supplier;		import java.util.function.Supplier;

			import org.apache.jena.vocabulary.OWL;
			import org.apache.jena.vocabulary.OWL2;
			import org.apache.jena.vocabulary.RDF;
	import org.semanticweb.HermiT.ReasonerFactory;		import org.semanticweb.HermiT.ReasonerFactory;
	import org.semanticweb.owl.explanation.api.Explanation;		import org.semanticweb.owl.explanation.api.Explanation;
	import org.semanticweb.owl.explanation.api.ExplanationGenerator;		import org.semanticweb.owl.explanation.api.ExplanationGenerator;
	@@ -65,6 +68,7 @@ import fr.emse.gitlab.saref.SAREFPipeline;
	import fr.emse.gitlab.saref.SAREFPipeline.Mode;		import fr.emse.gitlab.saref.SAREFPipeline.Mode;
	import fr.emse.gitlab.saref.entities.SAREFExample;		import fr.emse.gitlab.saref.entities.SAREFExample;
	import fr.emse.gitlab.saref.entities.SAREFVersion;		import fr.emse.gitlab.saref.entities.SAREFVersion;
			import fr.emse.gitlab.saref.entities.SAREFVersionName;
	import fr.emse.gitlab.saref.managers.parsers.JenaModelDocumentFormatFactory;		import fr.emse.gitlab.saref.managers.parsers.JenaModelDocumentFormatFactory;
	import fr.emse.gitlab.saref.managers.parsers.SourceOntologyParser;		import fr.emse.gitlab.saref.managers.parsers.SourceOntologyParser;

src/main/java/fr/emse/gitlab/saref/managers/RepositoryFactory.java

+22 −2

Original line number	Original line	Diff line number	Diff line
	@@ -33,6 +33,7 @@ import java.util.Map;
	import java.util.regex.Matcher;		import java.util.regex.Matcher;
	import java.util.regex.Pattern;		import java.util.regex.Pattern;

			import org.apache.jena.vocabulary.OWL2;
	import org.eclipse.jgit.api.Git;		import org.eclipse.jgit.api.Git;
	import org.eclipse.jgit.api.ListBranchCommand.ListMode;		import org.eclipse.jgit.api.ListBranchCommand.ListMode;
	import org.eclipse.jgit.api.errors.GitAPIException;		import org.eclipse.jgit.api.errors.GitAPIException;
	@@ -46,10 +47,12 @@ import fr.emse.gitlab.saref.SAREFPipeline.Mode;
	import fr.emse.gitlab.saref.SAREFPipelineException;		import fr.emse.gitlab.saref.SAREFPipelineException;
	import fr.emse.gitlab.saref.entities.SAREFCore;		import fr.emse.gitlab.saref.entities.SAREFCore;
	import fr.emse.gitlab.saref.entities.SAREFExtension;		import fr.emse.gitlab.saref.entities.SAREFExtension;
			import fr.emse.gitlab.saref.entities.SAREFNamedGraph;
	import fr.emse.gitlab.saref.entities.SAREFProject;		import fr.emse.gitlab.saref.entities.SAREFProject;
	import fr.emse.gitlab.saref.entities.SAREFRepository;		import fr.emse.gitlab.saref.entities.SAREFRepository;
	import fr.emse.gitlab.saref.entities.SAREFVersion;		import fr.emse.gitlab.saref.entities.SAREFVersion;
	import fr.emse.gitlab.saref.entities.SAREFVersionName;		import fr.emse.gitlab.saref.entities.SAREFVersionName;
			import fr.emse.gitlab.saref.utils.Languages;

	/**		/**
	* Reads the repository and all the branches		* Reads the repository and all the branches
	@@ -130,11 +133,15 @@ public class RepositoryFactory extends SAREFErrorLogger {
	final String msg = String.format(getMessage(MESSAGE.release_branch, originalBranch));		final String msg = String.format(getMessage(MESSAGE.release_branch, originalBranch));
	errorLogger.warn(msg);		errorLogger.warn(msg);
	throw new SAREFPipelineException(msg);		throw new SAREFPipelineException(msg);
	} else if (isTarget) {		}
			SAREFVersionName vn = guessVersion(project, directory);
			if (isTarget && vn == null) {
	final String msg = getMessage(MESSAGE.develop_branch, originalBranch);		final String msg = getMessage(MESSAGE.develop_branch, originalBranch);
	errorLogger.warn(msg);		errorLogger.warn(msg);
	}
	originalVersionName = SAREFVersionName.DEFAULT;		originalVersionName = SAREFVersionName.DEFAULT;
			} else {
			originalVersionName = vn;
			}
	} else {		} else {
	int major = Integer.parseInt(m.group(SAREF.REGEX_VERSION_MAJOR_VAR));		int major = Integer.parseInt(m.group(SAREF.REGEX_VERSION_MAJOR_VAR));
	int minor = Integer.parseInt(m.group(SAREF.REGEX_VERSION_MINOR_VAR));		int minor = Integer.parseInt(m.group(SAREF.REGEX_VERSION_MINOR_VAR));
	@@ -158,6 +165,19 @@ public class RepositoryFactory extends SAREFErrorLogger {
	}		}
	}		}

			private SAREFVersionName guessVersion(SAREFProject project, File directory) {
			try {
			File ontologyDirectory = new File(directory, "ontology");
			File ontologyFile = new File(ontologyDirectory, project.getOntologyFileName(Languages.TEXT_TURTLE));
			SAREFNamedGraph namedGraph = new SAREFNamedGraph("null");
			SAREF.loadModel(namedGraph, ontologyFile, errorLogger);
			String uri = namedGraph.getModel().listObjectsOfProperty(OWL2.versionIRI).next().asResource().getURI();
			return SAREF.extractVersionName(uri);
			} catch (Exception ex) {
			return null;
			}
			}

	private void readVersions(Git git, SAREFRepository repository) throws GitAPIException {		private void readVersions(Git git, SAREFRepository repository) throws GitAPIException {
	final List<Ref> allBranches;		final List<Ref> allBranches;
	final Pattern pattern;		final Pattern pattern;

src/main/java/fr/emse/gitlab/saref/managers/RepositoryManager.java

+2 −24

Original line number	Original line	Diff line number	Diff line
	@@ -185,7 +185,7 @@ public class RepositoryManager extends SAREFErrorLogger {
	} else {		} else {
	versionName = version.getVersionName().toString();		versionName = version.getVersionName().toString();
	}		}
	loadModel(version, ontologyFile, pipeline.getLogger(SAREF.getMessage("clause", repositoryName, versionName, "9.4.1")));		SAREF.loadModel(version, ontologyFile, pipeline.getLogger(SAREF.getMessage("clause", repositoryName, versionName, "9.4.1")));
	forEachTerm(version.getModel(), (term) -> {		forEachTerm(version.getModel(), (term) -> {
	if(term.getProject().equals(project)) {		if(term.getProject().equals(project)) {
	version.definesTerm(term);		version.definesTerm(term);
	@@ -202,7 +202,7 @@ public class RepositoryManager extends SAREFErrorLogger {
	}).forEach(p -> {		}).forEach(p -> {
	SAREFExample example = new SAREFExample(version, p);		SAREFExample example = new SAREFExample(version, p);
	File exampleFile = p.toFile();		File exampleFile = p.toFile();
	loadModel(example, exampleFile, pipeline.getLogger(SAREF.getMessage("clause_for", repositoryName, versionName, exampleFile, "9.6.1")));		SAREF.loadModel(example, exampleFile, pipeline.getLogger(SAREF.getMessage("clause_for", repositoryName, versionName, exampleFile, "9.6.1")));
	version.getExamples().put(example.getName(), example);		version.getExamples().put(example.getName(), example);
	forEachTerm(example.getModel(), (term) -> {		forEachTerm(example.getModel(), (term) -> {
	example.exemplifiesTerm(term);		example.exemplifiesTerm(term);
	@@ -214,28 +214,6 @@ public class RepositoryManager extends SAREFErrorLogger {
	}		}
	}		}


	private void loadModel(SAREFNamedGraph namedGraph, File file, Logger logger) {
	try (FileInputStream input = new FileInputStream(file)) {
	namedGraph.getModel().read(input, SAREF.BASE, Lang.TTL.getLabel());
	} catch (Exception ex) {
	if (ex instanceof RuntimeIOException && ex.getCause() instanceof MalformedInputException) {
	namedGraph.getModel().removeAll();
	try (InputStreamReader input2 = new InputStreamReader(new FileInputStream(file),
	Charset.defaultCharset())) {
	namedGraph.getModel().read(input2, SAREF.BASE, Lang.TTL.getLabel());
	} catch (Exception ex2) {
	namedGraph.getModel().removeAll();
	String msg = getMessage(MESSAGE.turtle, namedGraph.getIRI());
	logger.error(msg, ex2);
	}
	} else {
	String msg = getMessage(MESSAGE.turtle, namedGraph.getIRI());
	logger.error(msg, ex);
	}
	}
	}

	private void forEachTerm(Model model, Consumer<SAREFTerm> consumer) {		private void forEachTerm(Model model, Consumer<SAREFTerm> consumer) {
	model.listStatements().forEachRemaining(stmt -> {		model.listStatements().forEachRemaining(stmt -> {
	Resource s = stmt.getSubject();		Resource s = stmt.getSubject();

src/main/resources/messages/RepositoryManager.properties

+0 −1

Original line number	Original line	Diff line number	Diff line
	reset=Error when reseting repository to original branch %s		reset=Error when reseting repository to original branch %s
	checkout=Error when checking out version %s		checkout=Error when checking out version %s
	turtle=The document %s shall contain the sources of an ontology in the Turtle 1.1 format. See detailed error below.
	ioexception=Error while checking the `examples` directory for %s %s		ioexception=Error while checking the `examples` directory for %s %s
	load_exception=Error while loading the repository %s		load_exception=Error while loading the repository %s