Java tutorial
/** * PODD is an OWL ontology database used for scientific project management * * Copyright (C) 2009-2013 The University Of Queensland * * This program is free software: you can redistribute it and/or modify it under the terms of the * GNU Affero General Public License as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License along with this program. * If not, see <http://www.gnu.org/licenses/>. */ package com.github.podd.resources; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.io.StringReader; import java.io.StringWriter; import java.net.SocketTimeoutException; import java.nio.charset.Charset; import java.nio.file.Files; import java.nio.file.Path; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Objects; import java.util.Set; import java.util.Timer; import java.util.TimerTask; import java.util.UUID; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Future; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.SAXParser; import javax.xml.parsers.SAXParserFactory; import org.apache.commons.io.IOUtils; //import org.apache.commons.io.IOUtils; import org.openrdf.model.Literal; import org.openrdf.model.Model; import org.openrdf.model.URI; import org.openrdf.model.Value; import org.openrdf.model.ValueFactory; import org.openrdf.model.impl.LinkedHashModel; import org.openrdf.model.vocabulary.RDFS; import org.openrdf.queryrender.RenderUtils; import org.openrdf.rio.RDFFormat; import org.openrdf.rio.RDFHandlerException; import org.openrdf.rio.RDFParseException; import org.openrdf.rio.Rio; import org.openrdf.rio.UnsupportedRDFormatException; import org.restlet.Context; import org.restlet.data.CharacterSet; import org.restlet.data.CookieSetting; import org.restlet.data.Form; import org.restlet.data.MediaType; import org.restlet.data.Status; import org.restlet.representation.InputRepresentation; import org.restlet.representation.ReaderRepresentation; import org.restlet.representation.Representation; import org.restlet.resource.ClientResource; import org.restlet.resource.ResourceException; import org.restlet.util.Series; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.w3c.dom.Document; import org.w3c.dom.NamedNodeMap; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import com.github.ansell.propertyutil.PropertyUtil; import com.github.ansell.restletutils.RestletUtilMediaType; import com.github.ansell.restletutils.RestletUtilRole; import com.github.ansell.restletutils.SesameRealmConstants; import com.github.podd.api.DanglingObjectPolicy; import com.github.podd.api.DataReferenceVerificationPolicy; import com.github.podd.api.data.DataReference; import com.github.podd.api.data.DataReferenceConstants; import com.github.podd.exception.PoddException; import com.github.podd.ontologies.PODDBASE; import com.github.podd.ontologies.PODDSCIENCE; import com.github.podd.utils.InferredOWLOntologyID; import com.github.podd.utils.OntologyUtils; import com.github.podd.utils.PODD; import com.github.podd.utils.PoddRoles; import com.github.podd.utils.PoddUser; import com.github.podd.utils.PoddWebConstants; /** * Restlet based PODD Client implementation. * * @author Peter Ansell p_ansell@yahoo.com */ public class RestletPoddClientImpl implements PoddClient, Runnable { protected final Logger log = LoggerFactory.getLogger(this.getClass()); public final static String DEFAULT_PROPERTY_BUNDLE = "poddclient"; public static final String PROP_PODD_SERVER_URL = "podd.serverurl"; public static final String DEFAULT_PODD_SERVER_URL = null;// "http://localhost:8080/podd/"; public static final String PROP_PODD_USERNAME = "podd.username"; public static final String PROP_PODD_PASSWORD = "podd.password"; public final static String TEMP_UUID_PREFIX = "urn:temp:uuid:"; public final static String PATH_SPARQL2 = "sparql2"; private Series<CookieSetting> currentCookies = new Series<CookieSetting>(CookieSetting.class); private PropertyUtil props; private volatile String serverUrl = null; /** * Shortcut to {@link PODD#VF} */ protected final static ValueFactory vf = PODD.VF; public RestletPoddClientImpl() { this.props = new PropertyUtil(RestletPoddClientImpl.DEFAULT_PROPERTY_BUNDLE); } public RestletPoddClientImpl(final String poddServerUrl) { this(); String url = this.getProps().get(RestletPoddClientImpl.PROP_PODD_SERVER_URL, null); if (url == null) { this.serverUrl = poddServerUrl; } else { this.serverUrl = url; } } @Override public void addRole(final String userIdentifier, final RestletUtilRole role, final InferredOWLOntologyID artifact) throws PoddException { this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_USER_ROLES)); resource.getCookies().addAll(this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_USER_IDENTIFIER, userIdentifier); final Map<RestletUtilRole, Collection<URI>> mappings = new HashMap<>(); final Collection<URI> artifacts = Arrays.asList(artifact.getOntologyIRI().toOpenRDFURI()); mappings.put(role, artifacts); final Model model = new LinkedHashModel(); PoddRoles.dumpRoleMappingsUser(mappings, model); final Representation post = this.postRdf(resource, model); try { final Model parsedStatements = this.parseRdf(post); if (!parsedStatements.contains(null, SesameRealmConstants.OAS_USERIDENTIFIER, PODD.VF.createLiteral(userIdentifier))) { this.log.warn("Role edit response did not seem to contain the user identifier"); } } catch (final IOException e) { try { throw new IOException("Could not parse results due to an IOException", e); } catch (IOException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } } @Override public InferredOWLOntologyID appendArtifact(final InferredOWLOntologyID ontologyIRI, final InputStream partialInputStream, final RDFFormat format) throws PoddException { return this.appendArtifact(ontologyIRI, partialInputStream, format, DanglingObjectPolicy.REPORT, DataReferenceVerificationPolicy.DO_NOT_VERIFY); } @Override public InferredOWLOntologyID appendArtifact(final InferredOWLOntologyID artifactID, final InputStream partialInputStream, final RDFFormat format, final DanglingObjectPolicy danglingObjectPolicy, final DataReferenceVerificationPolicy dataReferenceVerificationPolicy) throws PoddException { final InputRepresentation rep = new InputRepresentation(partialInputStream, MediaType.valueOf(format.getDefaultMIMEType())); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_ARTIFACT_EDIT)); resource.getCookies().addAll(this.currentCookies); this.log.debug("cookies: {}", this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_EDIT_WITH_REPLACE, Boolean.toString(false)); resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_IDENTIFIER, artifactID.getOntologyIRI().toString()); resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_VERSION_IDENTIFIER, artifactID.getVersionIRI().toString()); if (danglingObjectPolicy == DanglingObjectPolicy.FORCE_CLEAN) { resource.addQueryParameter(PoddWebConstants.KEY_EDIT_WITH_FORCE, "true"); } if (dataReferenceVerificationPolicy == DataReferenceVerificationPolicy.VERIFY) { resource.addQueryParameter(PoddWebConstants.KEY_EDIT_VERIFY_FILE_REFERENCES, "true"); } resource.addQueryParameter("format", format.getDefaultMIMEType()); // Request the results in Turtle to reduce the bandwidth final Representation post = resource.post(rep, MediaType.APPLICATION_RDF_TURTLE); try { final Model parsedStatements = this.parseRdf(post); final Collection<InferredOWLOntologyID> result = OntologyUtils.modelToOntologyIDs(parsedStatements, true, false); if (!result.isEmpty()) { return result.iterator().next(); } throw new Exception("Failed to verify that the artifact was uploaded correctly."); } catch (final Exception e) { System.out.println(e.toString()); } return null; } @Override public Map<InferredOWLOntologyID, InferredOWLOntologyID> appendArtifacts( final Map<InferredOWLOntologyID, Model> uploadQueue) throws PoddException { final ConcurrentMap<InferredOWLOntologyID, InferredOWLOntologyID> resultMap = new ConcurrentHashMap<>(); for (final Entry<InferredOWLOntologyID, Model> nextUpload : uploadQueue.entrySet()) { try { final StringWriter writer = new StringWriter(4096); Rio.write(nextUpload.getValue(), writer, RDFFormat.RDFJSON); final InferredOWLOntologyID newID = this.appendArtifact(nextUpload.getKey(), new ByteArrayInputStream(writer.toString().getBytes(Charset.forName("UTF-8"))), RDFFormat.RDFJSON); if (newID == null) { this.log.error("Did not find a valid result from append artifact: {}", nextUpload.getKey()); } else if (nextUpload.getKey().equals(newID)) { this.log.error("Result from append artifact was not changed, as expected. {} {}", nextUpload.getKey(), newID); } else { resultMap.putIfAbsent(nextUpload.getKey(), newID); } } catch (final RDFHandlerException e) { this.log.error("Found exception generating upload body: ", e); } } return resultMap; } @Override public boolean autologin() throws PoddException { final String username = this.getProps().get(RestletPoddClientImpl.PROP_PODD_USERNAME, null); final String password = this.getProps().get(RestletPoddClientImpl.PROP_PODD_PASSWORD, null); Objects.requireNonNull(username, "Cannot automatically login as username was not defined in poddclient.properties"); Objects.requireNonNull(password, "Cannot automatically login as password was not defined in poddclient.properties"); return this.login(username, password); } @Override public PoddUser createUser(final PoddUser user) throws PoddException { try { final Model model = new LinkedHashModel(); user.toModel(model, true); final ByteArrayOutputStream output = new ByteArrayOutputStream(4096); Rio.write(model, output, RDFFormat.RDFJSON); final InputRepresentation rep = new InputRepresentation(new ByteArrayInputStream(output.toByteArray()), MediaType.valueOf(RDFFormat.RDFJSON.getDefaultMIMEType())); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_USER_ADD)); resource.getCookies().addAll(this.currentCookies); this.log.debug("cookies: {}", this.currentCookies); resource.addQueryParameter("format", RDFFormat.RDFJSON.getDefaultMIMEType()); // Request the results in Turtle to reduce the bandwidth final Representation post = resource.post(rep, MediaType.APPLICATION_RDF_TURTLE); final Model parsedStatements = this.parseRdf(post); final PoddUser result = PoddUser.fromModel(model); return result; } catch (final IOException | RDFHandlerException | ResourceException e) { System.out.println(e.toString()); } return null; } @Override public boolean deleteArtifact(final InferredOWLOntologyID artifactId) throws PoddException { this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_ARTIFACT_DELETE)); resource.getCookies().addAll(this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_IDENTIFIER, artifactId.getOntologyIRI().toString()); if (artifactId.getVersionIRI() != null) { // FIXME: Versions are not supported in general by PODD, but they are important for // verifying the state of the client to allow for early failure in cases where the // client is out of date. resource.addQueryParameter("versionUri", artifactId.getVersionIRI().toString()); } resource.delete(); if (resource.getStatus().isSuccess()) { return true; } else { try { throw new Exception( "Failed to successfully delete artifact: " + artifactId.getOntologyIRI().toString()); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } return false; } public Representation doSPARQL2(final String queryString, final Collection<InferredOWLOntologyID> artifactIds) throws PoddException { this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_SPARQL)); resource.getCookies().addAll(this.currentCookies); final Form form = new Form(); form.add(PoddWebConstants.KEY_SPARQLQUERY, queryString); // TODO: Parse query to make sure it is syntactically valid before sending query resource.addQueryParameter(PoddWebConstants.KEY_SPARQLQUERY, queryString); try { final Representation get = resource.get(MediaType.APPLICATION_ALL_XML); /* try { String d = get.getText().replaceAll("(.*)version=(.*)", ""); String f = d.replaceAll("(.*)sparql(.*)", "").replaceAll("(.*)result(.*)", ""); System.out.println(f); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } */ try { DocumentBuilder dBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); InputStream in = IOUtils.toInputStream(get.getText()); Document doc = dBuilder.parse(in); System.out.println("\r\n" + "============================== \r\n" + " PODD Query Results \r\n" + "=============================="); if (doc.hasChildNodes()) { printNote(doc.getChildNodes()); } } catch (Exception e) { System.out.println(e.getMessage()); } return get; } catch (final ResourceException e) { if (e.getStatus().equals(Status.CLIENT_ERROR_PRECONDITION_FAILED)) { System.out.println(""); System.out.println("Error: Access denied in server " + this.serverUrl + " with the login credentials provided in ~/poddclient.properties."); // Precondition failed indicates that they do not have access to any artifacts, so // return empty results set return null; } System.out.println(e.toString()); } catch (final UnsupportedRDFormatException e) { // Attempt to retry the request once to avoid random restlet failures stopping the // entire process try { final Representation get = resource.post(form.getWebRepresentation(CharacterSet.UTF_8), RestletUtilMediaType.APPLICATION_RDF_JSON); // Pass the desired format to the get method of the ClientResource // final Representation get = // resource.get(RestletUtilMediaType.APPLICATION_RDF_JSON); final StringWriter writer = new StringWriter(4096); get.write(writer); return null; } catch (final ResourceException e1) { if (e1.getStatus().equals(Status.CLIENT_ERROR_PRECONDITION_FAILED)) { System.out.println(""); System.out.println("Error: Access denied in server " + this.serverUrl + " with login credentials provided in ~/poddclient.properties."); // Precondition failed indicates that they do not have access to any artifacts, // so // return empty results set return null; } else { System.out.println(e.toString()); } } catch (final IOException | UnsupportedRDFormatException e1) { System.out.println(e.toString()); } } return null; } public Representation doSPARQL3(final String queryString, final Collection<InferredOWLOntologyID> artifactIds) throws PoddException { this.log.debug("cookies: {}", this.currentCookies); //final Context context = new Context(); //context.getParameters().add("socketTimeout", "10000"); //context.getParameters().add("connectionTimeout", "10000"); final ClientResource resource = new ClientResource(this.getUrl(PATH_SPARQL2)); resource.getCookies().addAll(this.currentCookies); final Form form = new Form(); form.add(PoddWebConstants.KEY_SPARQLQUERY, queryString); // TODO: Parse query to make sure it is syntactically valid before sending query resource.addQueryParameter(PoddWebConstants.KEY_SPARQLQUERY, queryString); try { final Representation get = resource.get(MediaType.APPLICATION_ALL_XML); /* try { String d = get.getText().replaceAll("(.*)version=(.*)", ""); String f = d.replaceAll("(.*)sparql(.*)", "").replaceAll("(.*)result(.*)", ""); System.out.println(f); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } */ try { DocumentBuilder dBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); String d = get.getText().replaceAll("(.*)version=(.*)", ""); String f = d.replaceAll("(.*)sparql(.*)", ""); InputStream in = IOUtils .toInputStream("<?xml version='1.0' encoding='UTF-8'?>" + " <r>" + f + " </r>", "UTF-8"); Document doc = dBuilder.parse(in); System.out.println("\r\n" + "============================== \r\n" + " PODD Query Results \r\n" + "=============================="); if (doc.hasChildNodes()) { printNote3(doc.getChildNodes()); } } catch (Exception e) { System.out.println(e.getMessage()); } return get; } catch (final ResourceException e) { if (e.getStatus().equals(Status.CLIENT_ERROR_PRECONDITION_FAILED)) { System.out.println(""); System.out.println("Error: Access denied in server " + this.serverUrl + " with the login credentials provided in ~/poddclient.properties."); // Precondition failed indicates that they do not have access to any artifacts, so // return empty results set return null; } System.out.println(e.toString()); } catch (final UnsupportedRDFormatException e) { // Attempt to retry the request once to avoid random restlet failures stopping the // entire process try { final Representation get = resource.post(form.getWebRepresentation(CharacterSet.UTF_8), RestletUtilMediaType.APPLICATION_RDF_JSON); // Pass the desired format to the get method of the ClientResource // final Representation get = // resource.get(RestletUtilMediaType.APPLICATION_RDF_JSON); final StringWriter writer = new StringWriter(4096); get.write(writer); return null; } catch (final ResourceException e1) { if (e1.getStatus().equals(Status.CLIENT_ERROR_PRECONDITION_FAILED)) { System.out.println(""); System.out.println("Error: Access denied in server " + this.serverUrl + " with login credentials provided in ~/poddclient.properties."); // Precondition failed indicates that they do not have access to any artifacts, // so // return empty results set return null; } else { System.out.println("Error: Unable to find the requested data in PODD"); System.out.println(e.toString()); } } catch (final IOException | UnsupportedRDFormatException e1) { System.out.println("Error: Unable to find the requested data in PODD"); System.out.println(e.toString()); return null; } } // Your database code here return null; } private static void printNote(NodeList nodeList) { for (int count = 0; count < nodeList.getLength(); count++) { Node tempNode = nodeList.item(count); // make sure it's element node. if (tempNode.getNodeType() == Node.ELEMENT_NODE) { // get node name and value if (!tempNode.getNodeName().startsWith("rdf:") && tempNode.getTextContent().length() > 0) { if (tempNode.getNodeName().startsWith("rdfs:label")) { System.out.println("Name" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("rdfs:comment")) { System.out.println("Description" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasPotColumnNumberOverall")) { System.out.println("Lane" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasPotPositionTray")) { System.out.println("Position" + ": " + tempNode.getTextContent()); } else { System.out.println(tempNode.getNodeName() + ": " + tempNode.getTextContent()); } } if (tempNode.hasChildNodes()) { // loop again if has child node printNote(tempNode.getChildNodes()); System.out.println(""); } } } } private static void printNote3(NodeList nodeList) { for (int count = 0; count < nodeList.getLength(); count++) { Node tempNode = nodeList.item(count); // make sure it's element node. if (tempNode.getNodeType() == Node.ELEMENT_NODE) { // get node name and value if (tempNode.getNodeName().startsWith("binding")) { if (tempNode.getAttributes().getNamedItem("name").getTextContent().equals("Experiment")) { System.out.println(""); System.out.print(tempNode.getAttributes().getNamedItem("name").getTextContent() + " : \t"); } else { System.out.print(tempNode.getAttributes().getNamedItem("name").getTextContent() + " : \t"); } } else if (tempNode.getNodeName().startsWith("literal")) { System.out.println(tempNode.getTextContent()); System.out.println(""); } else if (tempNode.getNodeName().startsWith("hasPotColumnNumberOverall")) { System.out.println("Lane" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasPotPositionTray")) { System.out.println("Position" + ": " + tempNode.getTextContent()); } else { //System.out.println(tempNode.getNodeName() + ": " + tempNode.getTextContent()); } if (tempNode.hasChildNodes()) { // loop again if has child node printNote3(tempNode.getChildNodes()); //System.out.println(""); } } } } private static void printNote2(NodeList nodeList, int prevValue) { for (int count = 0; count < nodeList.getLength(); count++) { Node tempNode = nodeList.item(count); // make sure it's element node. if (tempNode.getNodeType() == Node.ELEMENT_NODE) { // get node name and value if (!tempNode.getNodeName().startsWith("rdf:") && tempNode.getTextContent().length() > 0) { if (tempNode.getNodeName().startsWith("rdfs:label")) { System.out.println("Name" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("rdfs:comment")) { System.out.println("Description" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasPotColumnNumberOverall")) { System.out.println("Lane" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasPotPositionTray")) { System.out.println("Position" + ": " + tempNode.getTextContent()); } else if (tempNode.getNodeName().startsWith("hasValue")) { //if //prevValue = Integer.parseInt(tempNode.getNodeValue()); } else { System.out.println(tempNode.getNodeName() + ": " + tempNode.getTextContent()); } } if (tempNode.hasChildNodes()) { // loop again if has child node printNote(tempNode.getChildNodes()); System.out.println(""); } } } } @Override public Model downloadArtifact(final InferredOWLOntologyID artifactId) throws PoddException { try { final Path tempFile = Files.createTempFile("downloadartifact-", ".rj"); try (final OutputStream output = Files.newOutputStream(tempFile);) { this.downloadArtifact(artifactId, output, RDFFormat.RDFJSON); } try (final InputStream input = Files.newInputStream(tempFile);) { return Rio.parse(input, "", RDFFormat.RDFJSON); } } catch (RDFParseException | UnsupportedRDFormatException | IOException e) { System.out.println(e.toString()); } return null; } @Override public void downloadArtifact(final InferredOWLOntologyID artifactId, final OutputStream outputStream, final RDFFormat format) throws PoddException { Objects.requireNonNull(artifactId); Objects.requireNonNull(outputStream); Objects.requireNonNull(format); this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_ARTIFACT_GET_BASE)); resource.getCookies().addAll(this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_IDENTIFIER, artifactId.getOntologyIRI().toString()); if (artifactId.getVersionIRI() != null) { // FIXME: Versions are not supported in general by PODD, but they are important for // verifying the state of the client to allow for early failure in cases where the // client is out of date. resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_VERSION_IDENTIFIER, artifactId.getVersionIRI().toString()); } // Pass the desired format to the get method of the ClientResource final Representation get = resource.get(MediaType.valueOf(format.getDefaultMIMEType())); try { get.write(outputStream); } catch (final IOException e) { } } @Override public Model getObjectByURI(final URI objectURI, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_URI, RenderUtils.getSPARQLQueryString(objectURI)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByType(final URI type, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_TYPE_WITH_LABEL, RenderUtils.getSPARQLQueryString(type)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByTypeAndPrefix(final URI type, final String labelPrefix, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_TYPE_LABEL_STRSTARTS, RenderUtils.escape(labelPrefix), RenderUtils.getSPARQLQueryString(type)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByPredicate(final URI predicate, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String predicateString = RenderUtils.getSPARQLQueryString(predicate); // NOTE: predicateString must be both the second and third arguments sent into String.format // as it is used twice, once for the Construct and once for the Where // Hypothetically the second could be different to the third for mapping predicates, but // that would cause confusion if not obvious final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_PREDICATE, predicateString, predicateString); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByTypePredicateAndPrefix(final URI type, final URI predicate, final String labelPrefix, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String predicateString = RenderUtils.getSPARQLQueryString(predicate); // NOTE: predicateString must be both the second and third arguments sent into String.format // as it is used twice, once for the Construct and once for the Where // Hypothetically the second could be different to the third for mapping predicates, but // that would cause confusion if not obvious final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_TYPE_LABEL_STRSTARTS_PREDICATE, predicateString, predicateString, RenderUtils.escape(labelPrefix), RenderUtils.getSPARQLQueryString(type)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByTypeAndBarcode(final URI type, final String barcode, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_BARCODE_STRSTARTS, RenderUtils.escape(barcode), RenderUtils.getSPARQLQueryString(type)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getAllBarcodes(final Collection<InferredOWLOntologyID> artifacts) { try { return this.doSPARQL(PoddClient.TEMPLATE_SPARQL_BY_BARCODE_MATCH_NO_TYPE_NO_BARCODE, artifacts); } catch (PoddException e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; } @Override public Model getObjectsByBarcode(final String barcode, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_BARCODE_MATCH_NO_TYPE, RenderUtils.escape(barcode)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } @Override public Model getObjectsByTypeAndParent(final URI parent, final URI parentPredicate, final URI type, final Collection<InferredOWLOntologyID> artifacts) throws PoddException { final String queryString = String.format(PoddClient.TEMPLATE_SPARQL_BY_TYPE_AND_PARENT_ALL_PROPERTIES, RenderUtils.getSPARQLQueryString(parent), RenderUtils.getSPARQLQueryString(parentPredicate), RenderUtils.getSPARQLQueryString(type)); this.log.debug("queryString={}", queryString); return this.doSPARQL(queryString, artifacts); } /* * (non-Javadoc) * * @see com.github.podd.client.api.PoddClient#getPoddServerUrl() */ @Override public String getPoddServerUrl() { String result = this.serverUrl; if (result == null) { synchronized (this) { result = this.serverUrl; if (result == null) { this.serverUrl = this.props.get(RestletPoddClientImpl.PROP_PODD_SERVER_URL, RestletPoddClientImpl.DEFAULT_PODD_SERVER_URL); } result = this.serverUrl; } } return result; } public PropertyUtil getProps() { return this.props; } public URI getTempURI(final String tempUriString) { return RestletPoddClientImpl.vf .createURI(RestletPoddClientImpl.TEMP_UUID_PREFIX + tempUriString + UUID.randomUUID().toString()); } /** * Creates the URL for a given path using the current {@link #getPoddServerUrl()} result, or * throws an IllegalStateException if the server URL has not been set. * * @param path * The path of the web service to get a full URL for. * @return The full URL to the given path. * @throws IllegalStateException * If {@link #setPoddServerUrl(String)} has not been called with a valid URL before * this point. */ private String getUrl(final String path) { if (this.getPoddServerUrl() == null) { throw new IllegalStateException("PODD Server URL has not been set for this client"); } if (path == null || path.isEmpty()) { throw new NullPointerException("Path cannot be null or empty"); } String actualPath = path; final boolean serverUrlEndsWithSlash = this.serverUrl.endsWith("/"); // Avoid double slashes if (actualPath.startsWith("/") && serverUrlEndsWithSlash) { actualPath = actualPath.substring(1); } else if (!serverUrlEndsWithSlash) { actualPath = "/" + actualPath; } final String result = this.serverUrl + actualPath; this.log.debug("getURL={}", result); return result; } @Override public boolean isLoggedIn() { return !this.currentCookies.isEmpty(); } @Override public Map<RestletUtilRole, Collection<String>> listRoles(final InferredOWLOntologyID artifactId) throws PoddException { final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_ARTIFACT_ROLES)); resource.getCookies().addAll(this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_ARTIFACT_IDENTIFIER, artifactId.getOntologyIRI().toString()); this.log.debug("cookies: {}", this.currentCookies); final Representation get = resource.get(MediaType.APPLICATION_RDF_TURTLE); try { return PoddRoles.extractRoleMappingsArtifact(this.parseRdf(get)); } catch (final IOException e) { System.out.println(e.toString()); } return null; } @Override public Map<RestletUtilRole, Collection<URI>> listRoles(final String userIdentifier) throws PoddException { final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_USER_ROLES)); resource.getCookies().addAll(this.currentCookies); if (userIdentifier != null) { resource.addQueryParameter(PoddWebConstants.KEY_USER_IDENTIFIER, userIdentifier); } this.log.debug("cookies: {}", this.currentCookies); final Representation get = resource.get(MediaType.APPLICATION_RDF_TURTLE); try { return PoddRoles.extractRoleMappingsUser(this.parseRdf(get)); } catch (final IOException e) { System.out.println(e.toString()); } return null; } @Override public List<PoddUser> listUsers() throws PoddException { // Implement this when the service is available throw new RuntimeException("TODO: Implement listUsers!"); } /* * (non-Javadoc) * * @see com.github.podd.client.api.PoddClient#login(java.lang.String, char[]) */ @Override public boolean login(final String username, final String password) throws PoddException { final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.DEF_PATH_LOGIN_SUBMIT)); //final ClientResource resource = new ClientResource("https://poddtest.plantphenomics.org.au/podd/login"); resource.getCookies().addAll(this.currentCookies); // TODO: when Cookies natively supported by Client Resource, or another method remove this // Until then, this is necessary to manually attach the cookies after login to the // redirected address. // GitHub issue for this: https://github.com/restlet/restlet-framework-java/issues/21 resource.setFollowingRedirects(false); final Form form = new Form(); form.add("username", username); form.add("password", password); try { final Representation rep = resource.post(form.getWebRepresentation(CharacterSet.UTF_8)); if (rep != null) { // FIXME: Representation.getText may be implemented badly, so avoid calling it this.log.debug("login result: {}", rep.getText()); } else { this.log.debug("login result was null"); } // HACK if (resource.getStatus().equals(Status.REDIRECTION_SEE_OTHER) || resource.getStatus().isSuccess()) { this.currentCookies = resource.getCookieSettings(); } this.log.debug("cookies: {}", this.currentCookies); return !this.currentCookies.isEmpty(); } catch (final Throwable e) { this.currentCookies.clear(); System.out.println(""); System.out.println("Error: Unable to login to server " + this.serverUrl + " with login credentials provided in ~/poddclient.properties, incorrect username or password."); System.out.println(""); System.out.println(""); this.log.warn("Error with request", e); } return false; } /* * (non-Javadoc) * * @see com.github.podd.client.api.PoddClient#logout() */ @Override public boolean logout() throws PoddException { this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.DEF_PATH_LOGOUT)); // add the cookie settings so that the server knows who to logout resource.getCookies().addAll(this.currentCookies); // TODO: when Cookies natively supported by Client Resource, or another method remove this // Until then, this is necessary to manually attach the cookies after login to the // redirected address. // GitHub issue for this: https://github.com/restlet/restlet-framework-java/issues/21 resource.setFollowingRedirects(false); final Representation rep = resource.get(); this.currentCookies = resource.getCookieSettings(); try { this.log.info("logout result status: {}", resource.getStatus()); if (rep != null) { // FIXME: Representation.getText may be implemented badly, so avoid calling it // this.log.info("logout result: {}", rep.getText()); } else { this.log.info("logout result was null"); } this.log.info("cookies: {}", this.currentCookies); this.currentCookies.clear(); return true; } catch (final Throwable e) { this.log.warn("Error with request", e); } return false; } private Model parseRdf(final Representation rep) throws PoddException, IOException { final RDFFormat format = Rio.getParserFormatForMIMEType(rep.getMediaType().getName()); /* if(format == null) { throw new PoddException("Did not understand the format for the RDF response: " + rep.getMediaType().getName()); } */ try { return Rio.parse(rep.getStream(), "", format); } catch (RDFParseException | UnsupportedRDFormatException e) { System.out.println(e.toString()); } return null; } /** * @param resource * @param rdf * @return * @throws PoddException * @throws ResourceException */ private Representation postRdf(final ClientResource resource, final Model rdf) throws PoddException, ResourceException { final StringWriter writer = new StringWriter(); try { Rio.write(rdf, writer, RDFFormat.RDFJSON); } catch (final RDFHandlerException e) { } final Representation rep = new ReaderRepresentation(new StringReader(writer.toString()), RestletUtilMediaType.APPLICATION_RDF_JSON); final Representation post = resource.post(rep, RestletUtilMediaType.APPLICATION_RDF_JSON); return post; } @Override public InferredOWLOntologyID publishArtifact(final InferredOWLOntologyID ontologyIRI) throws PoddException { throw new RuntimeException("TODO: Implement publishArtifact!"); } @Override public void removeRole(final String userIdentifier, final RestletUtilRole role, final InferredOWLOntologyID artifact) throws PoddException { this.log.debug("cookies: {}", this.currentCookies); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_USER_ROLES)); resource.getCookies().addAll(this.currentCookies); resource.addQueryParameter(PoddWebConstants.KEY_USER_IDENTIFIER, userIdentifier); resource.addQueryParameter(PoddWebConstants.KEY_DELETE, "true"); final Map<RestletUtilRole, Collection<URI>> mappings = new HashMap<>(); final Collection<URI> artifacts = Arrays.asList(artifact.getOntologyIRI().toOpenRDFURI()); mappings.put(role, artifacts); final Model model = new LinkedHashModel(); PoddRoles.dumpRoleMappingsUser(mappings, model); final Representation post = this.postRdf(resource, model); try { final Model parsedStatements = this.parseRdf(post); if (!parsedStatements.contains(null, SesameRealmConstants.OAS_USERIDENTIFIER, PODD.VF.createLiteral(userIdentifier))) { this.log.warn("Role edit response did not seem to contain the user identifier"); } } catch (final IOException e) { } } /* * (non-Javadoc) * * @see com.github.podd.client.api.PoddClient#setPoddServerUrl(java.lang.String) */ @Override public void setPoddServerUrl(final String serverUrl) { this.serverUrl = serverUrl; } public void setProps(final PropertyUtil props) { this.props = props; } @Override public InferredOWLOntologyID unpublishArtifact(final InferredOWLOntologyID ontologyIRI) throws PoddException { throw new RuntimeException("TODO: Implement unpublishArtifact"); } @Override public InferredOWLOntologyID updateArtifact(final InferredOWLOntologyID ontologyIRI, final InputStream fullInputStream, final RDFFormat format) throws PoddException { throw new RuntimeException("TODO: Implement updateArtifact"); } @Override public InferredOWLOntologyID uploadNewArtifact(final Model model) throws PoddException { final ByteArrayOutputStream output = new ByteArrayOutputStream(); try { Rio.write(model, output, RDFFormat.RDFJSON); } catch (final RDFHandlerException e) { } return this.uploadNewArtifact(new ByteArrayInputStream(output.toByteArray()), RDFFormat.RDFJSON, DanglingObjectPolicy.REPORT, DataReferenceVerificationPolicy.DO_NOT_VERIFY); } @Override public InferredOWLOntologyID uploadNewArtifact(final InputStream input, final RDFFormat format) throws PoddException { return this.uploadNewArtifact(input, format, DanglingObjectPolicy.REPORT, DataReferenceVerificationPolicy.DO_NOT_VERIFY); } @Override public InferredOWLOntologyID uploadNewArtifact(final InputStream input, final RDFFormat format, final DanglingObjectPolicy danglingObjectPolicy, final DataReferenceVerificationPolicy dataReferenceVerificationPolicy) throws PoddException { final InputRepresentation rep = new InputRepresentation(input, MediaType.valueOf(format.getDefaultMIMEType())); final ClientResource resource = new ClientResource(this.getUrl(PoddWebConstants.PATH_ARTIFACT_UPLOAD)); resource.getCookies().addAll(this.currentCookies); this.log.debug("cookies: {}", this.currentCookies); resource.addQueryParameter("format", format.getDefaultMIMEType()); if (danglingObjectPolicy == DanglingObjectPolicy.FORCE_CLEAN) { resource.addQueryParameter(PoddWebConstants.KEY_EDIT_WITH_FORCE, "true"); } if (dataReferenceVerificationPolicy == DataReferenceVerificationPolicy.VERIFY) { resource.addQueryParameter(PoddWebConstants.KEY_EDIT_VERIFY_FILE_REFERENCES, "true"); } // Request the results in Turtle to reduce the bandwidth final Representation post = resource.post(rep, MediaType.APPLICATION_RDF_TURTLE); try { final Model parsedStatements = this.parseRdf(post); final Collection<InferredOWLOntologyID> result = OntologyUtils.modelToOntologyIDs(parsedStatements, true, false); if (!result.isEmpty()) { return result.iterator().next(); } } catch (final IOException e) { System.out.println(e.toString()); } return null; } @Override public Model doSPARQL(String queryString, Collection<InferredOWLOntologyID> artifacts) throws PoddException { // TODO Auto-generated method stub return null; } @Override public void run() { // TODO Auto-generated method stub } }