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//package fr.emse.gitlab.saref.jobs;
//
//import java.io.File;
//import java.io.FileOutputStream;
//import java.io.IOException;
//import java.nio.charset.StandardCharsets;
//import java.nio.file.Files;
//import java.nio.file.Path;
//import java.nio.file.Paths;
//import java.util.ArrayList;
//import java.util.HashSet;
//import java.util.Iterator;
//import java.util.List;
//import java.util.Set;
//
//import org.apache.commons.io.FileUtils;
//import org.apache.commons.io.IOUtils;
//import org.apache.jena.atlas.io.IndentedWriter;
//import org.apache.jena.graph.NodeFactory;
//import org.apache.jena.query.Dataset;
//import org.apache.jena.query.ReadWrite;
//import org.apache.jena.rdf.model.Model;
//import org.apache.jena.sparql.core.Var;
//import org.apache.jena.sparql.engine.binding.Binding;
//import org.apache.jena.sparql.engine.binding.BindingHashMap;
//import org.apache.jena.sparql.util.Context;
//import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
//
//import fr.emse.ci.sparqlext.SPARQLExt;
//import fr.emse.ci.sparqlext.engine.PlanFactory;
//import fr.emse.ci.sparqlext.engine.RootPlan;
//import fr.emse.ci.sparqlext.stream.LocationMapperAccept;
//import fr.emse.ci.sparqlext.stream.LocatorFileAccept;
//import fr.emse.ci.sparqlext.stream.LookUpRequest;
//import fr.emse.ci.sparqlext.stream.SPARQLExtStreamManager;
//import fr.emse.ci.sparqlext.utils.ContextUtils;
//import fr.emse.ci.sparqlext.utils.VarUtils;
//import fr.emse.gitlab.saref.Constants;
//import fr.emse.gitlab.saref.entities.tests.TestSuite;
//import fr.emse.gitlab.saref.entities.tests.TestSuites;
//import fr.emse.gitlab.saref.vocabs.EX;
//
//public class CreateDocumentation extends JobRunner {
// private final SPARQLExtStreamManager streamManager;
// public CreateDocumentation(String testSuiteName, SPARQLExtStreamManager streamManager) {
// super(testSuiteName);
// this.streamManager = streamManager;
// public void doJob(Dataset dataset, File directory) {
// dataset.begin(ReadWrite.READ);
// for (Iterator<String> it = dataset.listNames(); it.hasNext();) {
// String name = it.next();
// if (name.equals(EX.config)) {
// continue;
// }
// Model model = dataset.getNamedModel(name);
// try (IndentedWriter writer = new IndentedWriter(new FileOutputStream(new File(SITE_DIR, fileName + ".html")));) {
// Context context = ContextUtils.build(writer).setBase(Constants.BASE).setDebugTemplate(Constants.PRODUCTION).setInputDataset(dataset)
// .setStreamManager(sm)
// .build();
// BindingHashMap binding = new BindingHashMap();
// binding.add(VAR_GRAPH, NodeFactory.createURI(name));
// List<Binding> bindings = new ArrayList()<>();
// bindings.add(binding);
// planForTerm.execTemplateStream(bindings, context);
// }
// }
// dataset.end();
// }
//
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//
//
//// static final Logger LOG = LoggerFactory.getLogger(Documentation.class);
////
//// static final Gson gson = new Gson();
////
//// static final Pattern REGEX_REPO_PATTERN = Pattern.compile("^saref(-core|4[a-z][a-z][a-z][a-z])$", Pattern.CASE_INSENSITIVE);
////
//// static final File GIT_DIR = new File("target/sources");
//// static final File SITE_DIR = new File("target/site");
//// static final File STATIC_TARGET_DIR = new File("target/site/static");
//// static final String DATASET_DIR = "target/tdb";
////
//// static final String NS = "https://saref.etsi.org/";
//// private static final String REGEX_EXT = "(?<ext>core|saref4[a-z][a-z][a-z][a-z])";
//// private static final String REGEX_VERSION = "v(?<major>[1-9][0-9]*)\\.(?<minor>[0-9]+)\\.(?<patch>[0-9]+)";
////
//// private static final String REGEX_RELEASE_BRANCH = "^refs/remotes/origin/release-" + REGEX_VERSION + "$";
//// private static final Pattern REGEX_RELEASE_BRANCH_PATTERN = Pattern.compile(REGEX_RELEASE_BRANCH);
////
//// private static final String REGEX_TERM_URI = "^" + NS + REGEX_EXT + "/(?<localName>[^/]+)$";
//// private static final Pattern REGEX_TERM_PATTERN = Pattern.compile(REGEX_TERM_URI);
////
//// private static final String REGEX_ONTO_URI = "^" + NS + REGEX_EXT + "/" + REGEX_VERSION + "/$";
//// private static final Pattern REGEX_ONTO_PATTERN = Pattern.compile(REGEX_ONTO_URI);
////
//// private static final String REGEX_EXT_URI = "^" + NS + REGEX_EXT + "/";
//// private static final Pattern REGEX_EXT_PATTERN = Pattern.compile(REGEX_EXT_URI);
////
//// private static Dataset dataset;
//// private static final Model config = ModelFactory.createDefaultModel();
//// private static final Map<String, Model> ngs = new HashMap<>();
////
//// private static final Resource ETSI_URL = ResourceFactory.createResource("https://www.etsi.org/");
//// private static final Resource ETSI_LICENSE = ResourceFactory
//// .createResource("https://forge.etsi.org/etsi-software-license");
////
//// private static final SimpleDateFormat SIMPLE_DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd");
////
//// static final String DOC_NS = NS + "documentation/";
//// private static final String TERM_QUERY = "term/main.rqg";
//// private static final Var VAR_GRAPH = VarUtils.allocVar("term");
////
//// static final String urlString = "https://forge.etsi.org/rep/api/v4/groups/saref";
////
//// static final boolean useTDB = true;
////
////
////
//// public static void main(String[] args) throws MalformedURLException, IOException {
//// // do we have a directory named ontology here ? if not, we assume that we are executing from a repo.
//// File ontologyDir = new File("ontology");
////
////
////
//// dataset = TDBFactory.createDataset(DATASET_DIR);
////// Model m = dataset.getNamedModel("https://saref.etsi.org/core/accomplishes");
////// m.write(System.out, "TTL");
//// try {
//// checkFolderStructure();
////
//// checkUnusedTerms();
////
//// checkNameConflicts();
////
//// Group group = readGroup();
////
//// cloneRepos(group);
////
////// Group group = new Group();
////// List<Project> projects = new ArrayList<>();
////// group.projects = projects;
//////
////// Project repo = new Project();
////// repo.name = "saref-core";
////// repo.directory = new File(GIT_DIR, repo.name);
////// repo.namespace = getNamespace(repo);
////// repo.prefix = getPrefix(repo);
////// projects.add(repo);
//////
////// repo = new Project();
////// repo.name = "saref4ener";
////// repo.directory = new File(GIT_DIR, repo.name);
////// repo.namespace = getNamespace(repo);
////// repo.prefix = getPrefix(repo);
////// projects.add(repo);
////
//// readRepos(group);
////
//// writeToTDBDataset();
////
//
////
//// SPARQLExtStreamManager sm = initializeStreamManager();
////
//// RootPlan planForTerm = createPlanForTerm(sm);
////
//// generateFiles(sm, planForTerm);
//// } finally {
//// dataset.close();
//// }
////
//// }
////
////
////
//// private static void checkFolderStructure() {
////
//// }
////
//// private static void checkUnusedTerms() {
//// /*
//// * Query to find terms that are not defined in any ontology:
//// *
//// * PREFIX ex: <http://example.org/> PREFIX rdfs:
//// * <http://www.w3.org/2000/01/rdf-schema#> SELECT ?term ?version WHERE {
//// *
//// * ?term ex:isUsedBy ?version . MINUS { ?term rdfs:isDefinedBy ?v2 . } }
//// *
//// */
//// }
////
//// private static void checkNameConflicts() {
//// /*
//// * Query to find local name conflicts in different ontologies
//// *
//// * PREFIX ex: <http://example.org/> PREFIX rdfs:
//// * <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT * WHERE {
//// *
//// * ?term1 ex:localName ?name ; rdfs:isDefinedBy ?v1 . ?term2 ex:localName ?name
//// * ; rdfs:isDefinedBy ?v2 . FILTER( ?term1 != ?term2 ) }
//// *
//// */
//// }
////
////
//// private static Group readGroup() throws IOException {
//// final URL url = new URL(urlString);
//// InputStreamReader reader = new InputStreamReader(url.openStream());
//// return gson.fromJson(reader, Group.class);
//// }
////
//// private static void writeToTDBDataset() {
//// dataset.begin(ReadWrite.WRITE);
//// dataset.addNamedModel(EX.config, config);
//// for (String name : ngs.keySet()) {
//// dataset.addNamedModel(name, ngs.get(name));
//// }
////
//// Model defaultModel = dataset.getDefaultModel();
//// defaultModel.add(ResourceFactory.createResource("s"), ResourceFactory.createProperty("p"), ResourceFactory.createResource("o"));
//// dataset.commit();
//// }
////
//// private static void readRepos(Group group) throws IOException {
//// for (Project repo : group.projects) {
//// try (Git git = Git.open(repo.directory);) {
//// readRepo(repo, git);
//// }
//// }
//// }
////
//// static String getNamespace(String graphName) {
//// Matcher m = REGEX_EXT_PATTERN.matcher(graphName);
//// if (!m.find()) {
//// throw new IllegalArgumentException("got " + graphName);
//// }
//// return NS + m.group("ext") + "/";
//// }
////
//// static String getOntologyFileName(Project project) {
//// if (project.name.equals("saref-core")) {
//// return "saref.ttl";
//// } else {
//// return String.format("%s.ttl", project.name);
//// }
//// }
////
//// static String getNamespace(Project project) {
//// if (project.name.equals("saref-core")) {
//// return String.format("%score/", NS);
//// } else {
//// return String.format("%s%s/", NS, project.name);
//// }
//// }
////
//// static String getPrefix(String graphName) {
//// Matcher m = REGEX_EXT_PATTERN.matcher(graphName);
//// if (!m.find()) {
//// throw new IllegalArgumentException("got " + graphName);
//// }
//// String ext = m.group("ext");
//// if(ext.equals("core")) {
//// return "saref:";
//// } else {
//// String shortName = ext.substring(5);
//// return String.format("s%s:", shortName);
//// }
//// }
////
//// static String getPrefix(Project project) {
//// if (project.name.equals("saref-core")) {
//// return "saref:";
//// } else {
//// String shortName = project.name.substring(5);
//// return String.format("s%s:", shortName);
//// }
//// }
////
//// static String getVersionURI(Project project, Version version) {
//// if (project.name.equals("saref-core")) {
//// return String.format("%s%sv%s.%s.%s/", NS, "core/", version.major, version.minor, version.patch);
//// } else {
//// return String.format("%s%s/v%s.%s.%s/", NS, project.name, version.major, version.minor, version.patch);
//// }
//// }
////
//// static String getVersionPrefix(Project project, Version version) {
//// if (project.name.equals("saref-core")) {
//// return String.format("saref-%s.%s.%s:", version.major, version.minor, version.patch);
//// } else {
//// String shortName = project.name.substring(5);
//// return String.format("s%s-%s.%s.%s:", shortName, version.major, version.minor, version.patch);
//// }
//// }
////
//// private static void cloneRepos(Group group) throws IOException {
//// FileUtils.forceMkdir(GIT_DIR);
//// for (Project repo : new ArrayList<>(group.projects)) {
//// if (!REGEX_REPO_PATTERN.matcher(repo.name).matches()) {
//// group.projects.remove(repo);
//// continue;
//// }
//// repo.directory = new File(GIT_DIR, repo.name);
//// repo.namespace = getNamespace(repo);
//// repo.prefix = getPrefix(repo);
//// if (repo.directory.exists()) {
//// continue;
//// }
//// LOG.debug("Cloning project " + repo.name);
//// try (Git git = Git.cloneRepository().setURI(repo.http_url_to_repo).setDirectory(repo.directory).call()) {
//// } catch (Exception ex) {
//// LOG.warn("Could not clone project " + repo.name, ex);
//// }
//// }
//// }
////
//// private static void readRepo(Project repo, Git git) {
//// System.out.println("project" + repo.name);
////
//// repo.resource = ResourceFactory.createResource(repo.namespace);
//// config.add(repo.resource, RDF.type, OWL2.Ontology);
////
//// try {
//// List<Ref> remoteBranches = git.branchList().setListMode(ListBranchCommand.ListMode.REMOTE).call();
//// for (Ref ref : remoteBranches) {
//// String branch = ref.getName();
//// Matcher m = REGEX_RELEASE_BRANCH_PATTERN.matcher(branch);
//// if (!m.find()) {
//// continue;
//// }
//// Version version = new Version();
//// version.major = Integer.parseInt(m.group("major"));
//// version.minor = Integer.parseInt(m.group("minor"));
//// version.patch = Integer.parseInt(m.group("patch"));
//// version.uri = getVersionURI(repo, version);
//// version.resource = ResourceFactory.createResource(version.uri);
//// version.prefix = getVersionPrefix(repo, version);
//// version.ref = ref;
//// RevCommit commit = git.log().add(version.ref.getObjectId()).call().iterator().next();
//// version.issued = commit.getCommitterIdent().getWhen();
//// repo.releases.add(version);
//// System.out.println("version " + version);
//// }
////
//// // order versions
//// Collections.sort(repo.releases, (Version o1, Version o2) -> {
//// if (o1.major - o2.major != 0) {
//// return o1.major - o2.major;
//// }
//// if (o1.minor - o2.minor != 0) {
//// return o1.minor - o2.minor;
//// }
//// return o1.patch - o2.patch;
//// });
////
//// for (int i = 0; i < repo.releases.size(); i++) {
//// Version version = repo.releases.get(i);
////
//// Model onto = readOntology(repo, version);
//// ngs.put(version.uri, onto);
////
//// // compute some metadata
//// Version priorVersion = i == 0 ? null : repo.releases.get(i - 1);
//// addOntologyMetadata(onto, repo, git, version, priorVersion);
////
//// // for each term, add:
//// // some triples in the default graph
//// // -> used to detect naming clashes
//// // some triples in the named graph of the term
//// // -> used to display the page of the term
//// Set<Resource> definedTerms = new HashSet<>();
//// Set<Resource> usedTerms = new HashSet<>();
//// computeTerms(onto, repo, version, definedTerms, usedTerms);
//// config.add(repo.resource, EX.hasVersion, version.resource);
//// config.add(version.resource, RDF.type, EX.OntologyVersion);
//// config.add(version.resource, EX.versionInfo,
//// String.format("v%s.%s.%s", version.major, version.minor, version.patch));
//// if (priorVersion != null) {
//// config.add(version.resource, EX.priorVersion, priorVersion.resource);
//// }
////
//// for (Resource t : definedTerms) {
//// Model termModel = getNamedModel(t);
//// String localName = t.getURI().substring(repo.namespace.length());
//// termModel.add(t, RDFS.isDefinedBy, version.resource);
//// // keep the most recent definition of the term
//// if (i == repo.releases.size() - 1) {
//// termModel.add(t, DCTerms.modified, SIMPLE_DATE_FORMAT.format(version.issued),
//// XSDDatatype.XSDdate);
//// try (QueryExecution exec = QueryExecutionFactory.create("DESCRIBE <" + t.getURI() + ">",
//// onto)) {
//// termModel.add(exec.execDescribe());
//// }
//// }
//// config.add(t, RDF.type, RDFP.Resource);
//// config.add(t, EX.localName, localName);
//// config.add(t, RDFS.isDefinedBy, version.resource);
//// }
////
//// for (Resource t : usedTerms) {
//// Model termModel = getNamedModel(t);
//// termModel.add(t, EX.isUsedBy, version.resource);
//// config.add(t, RDF.type, RDFP.Resource);
//// config.add(t, EX.isUsedBy, version.resource);
//// }
//// }
//// } catch (Exception ex) {
//// LOG.warn("Exception for " + repo.name, ex);
//// }
//// }
////
//// private static Model readOntology(Project repo, Version version) throws Exception {
//// // checkout the HEAD of the release branch
//// Git.open(repo.directory).checkout().setName(version.ref.getName()).call();
//// Model onto = ModelFactory.createDefaultModel();
//// // read the ontology
//// File ontologyFile = new File(repo.directory, "ontology/" + getOntologyFileName(repo));
//// try (FileReader fr = new FileReader(ontologyFile)) {
//// onto.read(fr, NS, "TTL");
//// }
//// return onto;
//// }
////
//// private static void addOntologyMetadata(Model onto, Project repo, Git git, Version version, Version priorVersion)
//// throws Exception {
//// onto.add(repo.resource, RDF.type, OWL2.Ontology);
////
//// // we assume dc:title, dc:description, rdfs:comment, are defined, and have
//// // language tags
//// onto.removeAll(repo.resource, OWL2.versionIRI, null);
//// onto.add(repo.resource, OWL2.versionIRI, version.resource);
////
//// onto.removeAll(repo.resource, OWL2.versionInfo, null);
//// onto.add(repo.resource, OWL2.versionInfo,
//// String.format("v%s.%s.%s", version.major, version.minor, version.patch));
////
//// onto.removeAll(repo.resource, OWL2.priorVersion, null);
//// if (priorVersion != null) {
//// onto.add(repo.resource, OWL2.priorVersion, priorVersion.resource);
//// }
////
//// onto.removeAll(repo.resource, DCTerms.publisher, null);
//// onto.add(repo.resource, DCTerms.publisher, ETSI_URL);
////
//// onto.removeAll(repo.resource, DCTerms.license, null);
//// onto.add(repo.resource, DCTerms.license, ETSI_LICENSE);
////
//// // list of contributors
//// Set<Contributor> contributors = new HashSet<>();
//// for (Iterator<RevCommit> it = git.log().add(version.ref.getObjectId()).call().iterator(); it.hasNext();) {
//// RevCommit commit = it.next();
//// Contributor contributor = new Contributor(commit.getCommitterIdent());
//// contributors.add(contributor);
//// }
//// for (Contributor contributor : contributors) {
//// // git can only provide name + email.
//// // would need to maintain some list of mapping email -> url in the future.
//// Resource anon = onto.createResource();
//// onto.add(repo.resource, DCTerms.contributor, anon);
//// onto.add(anon, FOAF.name, contributor.getName());
//// onto.add(anon, FOAF.mbox, contributor.getEmailAddress());
//// }
////
//// // prefixes
//// onto.removeAll(repo.resource, VANN.preferredNamespacePrefix, null);
//// onto.removeAll(repo.resource, VANN.preferredNamespaceUri, null);
//// onto.add(repo.resource, VANN.preferredNamespacePrefix, repo.prefix);
//// onto.add(repo.resource, VANN.preferredNamespaceUri, repo.namespace, XSDDatatype.XSDanyURI);
////
//// // issued
//// onto.removeAll(repo.resource, DCTerms.issued, null);
//// onto.add(repo.resource, DCTerms.issued, SIMPLE_DATE_FORMAT.format(version.issued), XSDDatatype.XSDdate);
//// }
////
//// private static void computeTerms(Model onto, Project repo, Version version, Set<Resource> definedTerms,
//// Set<Resource> usedTerms) {
//// onto.listStatements().forEachRemaining(stmt -> {
//// Resource s = stmt.getSubject();
//// Resource p = stmt.getPredicate();
//// Resource o = stmt.getObject().isResource() ? (Resource) stmt.getObject() : null;
//// computeTerms(s, repo, version, definedTerms, usedTerms);
//// computeTerms(p, repo, version, definedTerms, usedTerms);
//// computeTerms(o, repo, version, definedTerms, usedTerms);
//// });
//// }
////
//// private static void computeTerms(Resource t, Project repo, Version version, Set<Resource> definedTerms,
//// Set<Resource> usedTerms) {
//// if (t == null || !t.isURIResource() || !t.getURI().startsWith(NS) || t.getURI().endsWith("/")) {
//// return;
//// }
//// String uri = t.getURI();
//// if (uri.startsWith(repo.namespace)) {
//// definedTerms.add(t);
//// } else if (!uri.startsWith(repo.namespace)) {
//// usedTerms.add(t);
//// }
//// }
////
//// private static Model getNamedModel(Resource t) {
//// String uri = t.getURI();
//// if (ngs.containsKey(uri)) {
//// return ngs.get(uri);
//// } else {
//// Model model = ModelFactory.createDefaultModel();
//// model.add(t, RDF.type, RDFS.Resource);
//// ngs.put(uri, model);
//// return model;
//// }
//// }
////
//// private static class EX {
////
//// private static String NS = "http://example.org/";
//// private static String config = NS + "config";
//// private static Property localName = ResourceFactory.createProperty(NS, "localName");
//// private static Property hasVersion = ResourceFactory.createProperty(NS, "hasVersion");
//// private static Property versionInfo = ResourceFactory.createProperty(NS, "versionInfo");
//// private static Property priorVersion = ResourceFactory.createProperty(NS, "priorVersion");
//// private static Property isUsedBy = ResourceFactory.createProperty(NS, "isUsedBy");
//// private static Resource OntologyVersion = ResourceFactory.createResource(NS + "OntologyVersion");
//// }
////
//// private static class VANN {
////
//// private static String NS = "http://purl.org/vocab/vann/";
//// private static Property preferredNamespacePrefix = ResourceFactory.createProperty(NS,
//// "preferredNamespacePrefix");
//// private static Property preferredNamespaceUri = ResourceFactory.createProperty(NS, "preferredNamespaceUri");
//// }
////
//// private static class RDFP {
//// public static final String NS = "https://w3id.org/rdfp/";
//// public static final Property presentedBy = ResourceFactory.createProperty(NS + "presentedBy");
//// public static final Property presentationFor = ResourceFactory.createProperty(NS + "presentationForq");
//// public static final Property loweringRule = ResourceFactory.createProperty(NS + "loweringRule");
//// public static final Property liftingRule = ResourceFactory.createProperty(NS + "liftingRule");
//// public static final Property validationRule = ResourceFactory.createProperty(NS + "validationRule");
//// public static final Resource Graph = ResourceFactory.createResource(NS + "Graph");
//// public static final Resource Resource = ResourceFactory.createResource(NS + "Resource");
//// public static final Property representedBy = ResourceFactory.createProperty(NS + "representedBy");
//// public static final Property mediaType = ResourceFactory.createProperty(NS + "mediaType");
//// public static final Property alias = ResourceFactory.createProperty(NS + "alias");
//// public static final Property describedBy = ResourceFactory.createProperty(NS + "describedBy");
//// public static final Property filePath = ResourceFactory.createProperty(NS + "filePath");
//// public static final Resource Ontology = ResourceFactory.createResource(NS + "Ontology");
//// public static final Property fileSelector = ResourceFactory.createProperty(NS + "fileSelector");
//// }
//
//}