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package fr.emse.gitlab.saref.jobs;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import java.nio.charset.MalformedInputException;
import java.nio.charset.StandardCharsets;
import java.text.SimpleDateFormat;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;
import org.apache.commons.io.IOUtils;
import org.apache.jena.atlas.RuntimeIOException;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.QuerySolutionMap;
import org.apache.jena.query.ReadWrite;
import org.apache.jena.query.ResultSet;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.NodeIterator;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.riot.Lang;
import org.apache.jena.update.UpdateExecutionFactory;
import org.apache.jena.update.UpdateFactory;
import org.apache.jena.update.UpdateProcessor;
import org.apache.jena.update.UpdateRequest;
import org.apache.jena.vocabulary.OWL2;
import org.apache.jena.vocabulary.RDF;
import org.topbraid.jenax.util.JenaUtil;
import org.topbraid.shacl.validation.ValidationUtil;
import org.topbraid.shacl.vocabulary.SH;
import fr.emse.gitlab.saref.Constants;
import fr.emse.gitlab.saref.SAREFPipelineException;
import fr.emse.gitlab.saref.entities.git.Version;
import fr.emse.gitlab.saref.vocabs.EX;
import fr.emse.gitlab.saref.vocabs.RDFP;
public class ReadExamples extends JobRunner {
static final String SHACL_WARNING = "http://www.w3.org/ns/shacl#Warning";
static final String SHACL_VIOLATION = "http://www.w3.org/ns/shacl#Violation";
public static final String REGEX_TERM_URI = "^" + Constants.BASE + Constants.REGEX_EXT + "/(?<localName>[^/]+)$";
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static final String SELECT_VIOLATION = "PREFIX sh: <http://www.w3.org/ns/shacl#>\n"
+ "SELECT ?focusNode ?resultMessage ?resultPath ?value ?severity\n" + "WHERE { \n"
+ " ?violation sh:focusNode ?focusNode .\n" + " ?violation sh:resultMessage ?resultMessage .\n"
+ " ?violation sh:resultSeverity ?severity .\n"
+ " OPTIONAL { ?violation sh:resultPath ?resultPath . }\n"
+ " OPTIONAL { ?violation sh:value ?value . } \n" + "}";
static final Map<String, String> PREFIXES = new HashMap<String, String>();
static {
PREFIXES.put("owl", "http://www.w3.org/2002/07/owl#");
PREFIXES.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
PREFIXES.put("xsd", "http://www.w3.org/2001/XMLSchema#");
PREFIXES.put("dcterms", "http://purl.org/dc/terms/");
PREFIXES.put("vann", "http://purl.org/vocab/vann/");
PREFIXES.put("foaf", "http://xmlns.com/foaf/0.1/");
PREFIXES.put("schema", "http://schema.org/");
PREFIXES.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
PREFIXES.put("voaf", "http://purl.org/vocommons/voaf#");
PREFIXES.put("dce", "http://purl.org/dc/elements/1.1/");
PREFIXES.put("dct", "http://purl.org/dc/terms/");
PREFIXES.put("xml", "http://www.w3.org/XML/1998/namespace/");
PREFIXES.put("saref", "https://saref.etsi.org/core/");
}
private static final SimpleDateFormat SIMPLE_DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd");
public ReadExamples(String testSuiteName) {
super(testSuiteName);
}
public void doJob(Dataset dataset, Version version, String url, File exampleFile) throws SAREFPipelineException {
Model model = ModelFactory.createDefaultModel();
try (FileInputStream input = new FileInputStream(exampleFile)) {
model.read(input, Constants.BASE, Lang.TTL.getLabel());
} catch (Exception ex) {
if(ex instanceof RuntimeIOException && ex.getCause() instanceof MalformedInputException) {
try (InputStreamReader input2 = new InputStreamReader(new FileInputStream(exampleFile), Charset.defaultCharset())) {
model.read(input2, Constants.BASE, Lang.TTL.getLabel());
} catch (Exception ex2) {
logger.error("Exception while reading the example file", ex);
throw new SAREFPipelineException("Exception while reading the example file", ex2);
}
} else {
logger.error("Exception while reading the example file", ex);
throw new SAREFPipelineException("Exception while reading the example file", ex);
}
}
checkPrefixes(model);
checkShapes(model, version);
Resource example = ResourceFactory.createResource(url);
dataset.begin(ReadWrite.WRITE);
Model config = getNamedModel(dataset, Constants.CONFIG);
try {
updateExampleMetadata(version, model, example);
} catch (Exception ex) {
logger.error("Error while updating example metadata", ex);
throw new SAREFPipelineException("Error while updating example metadata", ex);
}
dataset.addNamedModel(url, model);
augmentTermGraphs(dataset, version, example, model, config, exampleFile);
dataset.commit();
}
private void checkPrefixes(Model model) {
final Map<String, String> prefixes = model.getNsPrefixMap();
for (String s : PREFIXES.keySet()) {
if (prefixes.containsKey(s)) {
if (!prefixes.get(s).equals(PREFIXES.get(s))) {
logger.warn(String.format(
"Prefix `%s:` in the example file is expected to be equal to `<%s>`. Got: `<%s>`", s,
PREFIXES.get(s), prefixes.get(s)));
}
}
}
for (Map.Entry<String, String> entry : prefixes.entrySet()) {
String s = entry.getKey();
String l = entry.getValue();
if (l.contains("saref")) {
if (!l.matches(Constants.REGEX_ONTO_SERIES_URI)) {
logger.warn(String.format(
"Prefix `%s:` in the example file contains string \"saref\", but does not seem to match the official SAREF ontologies namespaces: `\\\\%s\\\\`. Got: `<%s>`",
s, Constants.REGEX_ONTO_SERIES_URI, l));
}
}
}
}
private void checkShapes(Model model, Version version) throws SAREFPipelineException {
Model shapeModel = JenaUtil.createDefaultModel();
try (InputStream in = ReadOntology.class.getClassLoader().getResourceAsStream("exampleShape.ttl")) {
shapeModel.read(in, Constants.BASE, "TTL");
} catch (Exception ex) {
logger.error("Exception while reading the example shape file", ex);
throw new SAREFPipelineException("Exception while reading the example shape file", ex);
}
Resource reportResource = ValidationUtil.validateModel(model, shapeModel, true);
boolean conforms = reportResource.getProperty(SH.conforms).getBoolean();
if (!conforms) {
Model reportModel = reportResource.getModel();
reportModel.setNsPrefixes(PREFIXES);
reportModel.setNsPrefix("sh", "http://www.w3.org/ns/shacl#");
try (QueryExecution exec = QueryExecutionFactory.create(SELECT_VIOLATION, reportModel);) {
for (ResultSet resultSet = exec.execSelect(); resultSet.hasNext();) {
QuerySolution sol = resultSet.next();
Resource severity = sol.getResource("severity");
Resource focusNode = sol.get("focusNode").asResource();
Literal resultMessage = sol.getLiteral("resultMessage");
RDFNode value = sol.get("value");
String gotString = (value != null && value.isURIResource()) ? String.format(" Got: %s", value)
: "";
if (severity != null && severity.getURI().equals(SHACL_VIOLATION)) {
logger.error(String.format("Shape violation on node %s: %s%s", focusNode, resultMessage,
gotString));
} else {
logger.warn(String.format("Shape violation on node %s: %s%s", focusNode, resultMessage,
gotString));
}
}
}
}
int onto = 0;
ResIterator it = model.listSubjectsWithProperty(RDF.type, OWL2.Ontology);
if(!it.hasNext()) {
logger.error("There shall be exactly one owl:Ontology");
}
while(it.hasNext()) {
Resource ontology = it.next();
if(onto++>1) {
logger.error("There shall be exactly one owl:Ontology");
}
// check that this ontology is imported (without a version)
boolean found = false;
NodeIterator its = model.listObjectsOfProperty(ontology, OWL2.imports);
while(its.hasNext()) {
RDFNode s = its.next();
String uri = s.asResource().getURI();
if(uri.equals(version.getRepository().getNamespace())) {
found = true;
// } else {
// if(!uri.matches("^https://saref.etsi.org/(core|saref4[a-z]{4})/v[1-9][0-9]*\\\\.[1-9][0-9]*\\\\.[1-9][0-9]*/$")) {
// logger.error("Only SAREF ontologies with specific versions shall be imported. Their URIs conform to the regular expression `^https://saref.etsi.org/(core|saref4[a-z]{4})/v[1-9][0-9]*\\\\.[1-9][0-9]*\\\\.[1-9][0-9]*/$`");
// }
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}
}
if(!found) {
logger.error(String.format("The current ontology shall be imported: <%s>", version.getRepository().getNamespace()));
}
}
}
private void updateExampleMetadata(Version version, Model model, Resource example) throws Exception {
Dataset dataset = DatasetFactory.create(model);
QuerySolutionMap sol = new QuerySolutionMap();
sol.add("IRI", example);
String updateString = IOUtils.toString(ReadExamples.class.getClassLoader().getResourceAsStream("queries/examples/updateOntologyIRI.rq"), StandardCharsets.UTF_8);
UpdateRequest updateRequest = UpdateFactory.create(updateString);
UpdateProcessor exec = UpdateExecutionFactory.create(updateRequest, dataset, sol);
exec.execute();
sol = new QuerySolutionMap();
sol.add("ONTOLOGY_SERIES", version.getRepository().getResource());
sol.add("ONTOLOGY_VERSION", version.getResource());
updateString = IOUtils.toString(ReadExamples.class.getClassLoader().getResourceAsStream("queries/examples/updateImportIRI.rq"), StandardCharsets.UTF_8);
updateRequest = UpdateFactory.create(updateString);
exec = UpdateExecutionFactory.create(updateRequest, dataset, sol);
exec.execute();
}
private void augmentTermGraphs(Dataset dataset, Version version, Resource example, Model model, Model config, File exampleFile) {
Set<Resource> exemplifiedTerms = new HashSet<>();
computeTerms(version, example, model, exemplifiedTerms);
config.add(example, RDF.type, EX.Example);
String localName = exampleFile.getName().substring(0,exampleFile.getName().length()-4);
config.add(example, EX.localName, localName);
for (Resource t : exemplifiedTerms) {
Model termModel = getNamedModel(dataset, t.getURI());
termModel.add(t, EX.hasExample, example);
config.add(t, RDF.type, RDFP.Resource);
config.add(t, EX.hasExample, example);
}
}
private void computeTerms(Version version, Resource example, Model model, Set<Resource> exemplifiedTerms) {
model.listStatements().forEachRemaining(stmt -> {
Resource s = stmt.getSubject();
Resource p = stmt.getPredicate();
Resource o = stmt.getObject().isResource() ? (Resource) stmt.getObject() : null;
computeTerms(version, example, s, exemplifiedTerms);
computeTerms(version, example, p, exemplifiedTerms);
computeTerms(version, example, o, exemplifiedTerms);
});
}
private void computeTerms(Version version, Resource example, Resource t, Set<Resource> exemplifiedTerms) {
if (t == null || !t.isURIResource() || !t.getURI().startsWith(Constants.BASE) || t.getURI().endsWith("/")) {
return;
}
String uri = t.getURI();
exemplifiedTerms.add(t);
}
// if (uri.startsWith(version.getRepository().getNamespace()) && !uri.startsWith(example.getURI())) {
// exemplifiedTerms.add(t);
// }
}
private Model getNamedModel(Dataset dataset, String uri) {
if (!dataset.containsNamedModel(uri)) {
dataset.addNamedModel(uri, ModelFactory.createDefaultModel());
}
return dataset.getNamedModel(uri);
}
}