# HG changeset patch # User dwinter # Date 1325504548 -3600 # Node ID aae47a713589ee9b88524b571996a982d5c55083 # Parent dfd72ea936ffec5302d2b2cb59d17f6c8509ce9d editing diff -r dfd72ea936ff -r aae47a713589 .classpath --- a/.classpath Thu Dec 29 15:19:29 2011 +0100 +++ b/.classpath Mon Jan 02 12:42:28 2012 +0100 @@ -12,6 +12,7 @@ + diff -r dfd72ea936ff -r aae47a713589 .settings/org.eclipse.wst.common.component --- a/.settings/org.eclipse.wst.common.component Thu Dec 29 15:19:29 2011 +0100 +++ b/.settings/org.eclipse.wst.common.component Mon Jan 02 12:42:28 2012 +0100 @@ -12,9 +12,6 @@ uses - - uses - uses @@ -135,6 +132,15 @@ uses + + uses + + + uses + + + uses + diff -r dfd72ea936ff -r aae47a713589 libs/org.json.jar Binary file libs/org.json.jar has changed diff -r dfd72ea936ff -r aae47a713589 libs/org.restlet.ext.jaas.jar Binary file libs/org.restlet.ext.jaas.jar has changed diff -r dfd72ea936ff -r aae47a713589 libs/org.restlet.ext.json.jar Binary file libs/org.restlet.ext.json.jar has changed diff -r dfd72ea936ff -r aae47a713589 src/de/mpiwg/itgroup/metaDataManagerRestlet/RestServer.java --- a/src/de/mpiwg/itgroup/metaDataManagerRestlet/RestServer.java Thu Dec 29 15:19:29 2011 +0100 +++ b/src/de/mpiwg/itgroup/metaDataManagerRestlet/RestServer.java Mon Jan 02 12:42:28 2012 +0100 @@ -1,19 +1,33 @@ package de.mpiwg.itgroup.metaDataManagerRestlet; +import java.net.URI; +import java.net.URISyntaxException; + +import javax.security.auth.callback.CallbackHandler; +import javax.security.auth.login.Configuration; + import org.apache.log4j.BasicConfigurator; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.restlet.Application; import org.restlet.Context; +import org.restlet.Request; +import org.restlet.Response; import org.restlet.Restlet; +import org.restlet.data.ChallengeScheme; +import org.restlet.ext.jaas.JaasVerifier; import org.restlet.routing.Router; import org.restlet.routing.Template; import org.restlet.routing.TemplateRoute; +import org.restlet.security.ChallengeAuthenticator; + +import com.sun.security.auth.login.ConfigFile; import de.mpiwg.itgroup.metaDataManagerRestlet.pid.PIDcreator; import de.mpiwg.itgroup.metaDataManagerRestlet.ui.GeneralInfo; import de.mpiwg.itgroup.metaDataManagerRestlet.ui.SearchPersons; import de.mpiwg.itgroup.metadataManager.indexMeta.server.IndexMetaProvider; +import de.mpiwg.itgroup.nimanager.edit.Editor; import de.mpiwg.itgroup.nimanager.persons.PersonByNameService; import de.mpiwg.itgroup.nimanager.persons.PersonByIDService; import de.mpiwg.itgroup.nimanager.persons.PersonListService; @@ -34,7 +48,74 @@ } + + private ChallengeAuthenticator authenticator; + private CallbackHandler callbackHandler; + + /** Erzeuge einen Authenticator + * @return + */ + private ChallengeAuthenticator createAuthenticator() { + Context context = getContext(); + boolean optional = true; + ChallengeScheme challengeScheme = ChallengeScheme.HTTP_BASIC; + String realm = "Annotation Service"; + + JaasVerifier verifier = new JaasVerifier("BasicJaasAuthenticationApplication"); + //JaasVerifier verifier = new JaasVerifier("DummyAuthentication"); + + Configuration jaasConfig; + jaasConfig = createConfiguration(); + + + verifier.setConfiguration(jaasConfig); + verifier.setUserPrincipalClassName("com.sun.security.auth.UserPrincipal"); + + ChallengeAuthenticator auth = new ChallengeAuthenticator(context, optional, challengeScheme, realm, verifier) { + @Override + protected boolean authenticate(Request request, Response response) { + if (request.getChallengeResponse() == null) { + return false; + } else { + return super.authenticate(request, response); + } + } + }; + + return auth; + } + + /** + * Konfiguration für den Authentificator in Jaas. Pfad zum JAAS-Konfigurationsfile liegt im Context-Parameter + * "de.mpiwg.itgroup.annotationManager.jaas.configFilePath". + * @return + */ + protected Configuration createConfiguration() { + Configuration jaasConfig; + URI confUri; + + Context context = getContext(); + String configFilePath = context.getParameters().getFirstValue("de.mpiwg.itgroup.jaas.configFilePath"); + + + try { + confUri = new URI(configFilePath); + } catch (URISyntaxException e) { + e.printStackTrace(); + confUri = null; + } + + jaasConfig= new ConfigFile(confUri); + return jaasConfig; + } + + + + + public synchronized Restlet createInboundRoot(){ + this.authenticator = createAuthenticator(); + Router router = new Router(getContext()); router.attach("/",GeneralInfo.class); @@ -45,11 +126,38 @@ router.attach("/person/id/{personId}",PersonService.class); router.attach("/person/id/{personId}/{graphId}",PersonService.class); router.attach("/ids",PersonByIDService.class); + router.attach("/edit",Editor.class); TemplateRoute route = router.attach("/indexMeta", IndexMetaProvider.class); route.setMatchingMode(Template.MODE_STARTS_WITH); + authenticator.setNext(router); + return authenticator; + + - return router; } + + /** + * Authentifiziere den Benutzer aus dem Request (BasicAuthenfication) + * @param request + * @param response + * @return + */ + public boolean authenticate(Request request, Response response) { + if (!request.getClientInfo().isAuthenticated()) { + authenticator.challenge(response, false); + return false; + } + + if(request.getClientInfo().getUser()==null) //FIXME sometimes ist authenticated true, but no user + { + authenticator.challenge(response, false); + return false; + } + + + return true; + } + } diff -r dfd72ea936ff -r aae47a713589 src/de/mpiwg/itgroup/nimanager/edit/Editor.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/de/mpiwg/itgroup/nimanager/edit/Editor.java Mon Jan 02 12:42:28 2012 +0100 @@ -0,0 +1,316 @@ +package de.mpiwg.itgroup.nimanager.edit; + +import java.io.UnsupportedEncodingException; +import java.net.URLDecoder; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import org.apache.commons.lang.StringUtils; +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.apache.log4j.lf5.util.StreamUtils; +import org.openrdf.model.Statement; +import org.openrdf.repository.RepositoryException; +import org.openrdf.repository.RepositoryResult; +import org.restlet.Context; +import org.restlet.data.ClientInfo; +import org.restlet.data.Form; +import org.restlet.data.MediaType; +import org.restlet.data.Status; +import org.restlet.engine.component.ChildContext; +import org.restlet.representation.Representation; +import org.restlet.representation.StringRepresentation; +import org.restlet.resource.Get; +import org.restlet.resource.Post; +import org.restlet.resource.ServerResource; +import org.restlet.security.User; + +import de.mpiwg.itgroup.metaDataManagerRestlet.RestServer; +import de.mpiwg.itgroup.triplestoremanager.exceptions.TripleStoreHandlerException; +import de.mpiwg.itgroup.triplestoremanager.owl.MetaDataHandler; +import de.mpiwg.itgroup.triplestoremanager.owl.TripleStoreHandler; +import de.mpiwg.itgroup.triplestoremanager.owl.TripleStoreHandler.LiteralQuadruple; +import de.mpiwg.itgroup.triplestoremanager.owl.TripleStoreHandler.Quadruple; +import edu.stanford.smi.protegex.owl.model.impl.DefaultRDFProperty; +import edu.stanford.smi.protege.model.DefaultCls; +/** + * @author dwinter + * + * Edit an Entity defined by OWL modell + */ +public class Editor extends ServerResource { + + private String NAMED_ENTITIES_ONTOLOGIE_URL = "http://ontologies.mpiwg-berlin.mpg.de/authorities/namedIdentities"; + private String VIRTUOSO_PW; + private String VIRTUOSO_USER; + private String virtuoso_server_url; + private String TRIPLE_INDEX_PATH; + private Logger rl = Logger.getRootLogger(); + private MetaDataHandler mh; + private TripleStoreHandler th; + private String editGraph="file:///personEdits.rdf"; + + + public Editor (){ + ChildContext context = (ChildContext)Context.getCurrent(); + virtuoso_server_url = context.getParameters().getFirstValue("de.mpwig.itgroup.personSearch.virtuoso.url"); + VIRTUOSO_PW = context.getParameters().getFirstValue("de.mpwig.itgroup.personSearch.virtuoso.pw"); + VIRTUOSO_USER = context.getParameters().getFirstValue("de.mpwig.itgroup.personSearch.virtuoso.user"); + rl.setLevel(Level.DEBUG); + try { + th = TripleStoreHandler.getInstance(virtuoso_server_url, VIRTUOSO_USER, VIRTUOSO_PW); + + //th = new TripleStoreHandler(virtuoso_server_url, VIRTUOSO_USER, VIRTUOSO_PW); + } catch (TripleStoreHandlerException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + mh = MetaDataHandler.getInstance(); + } + + public Editor(String serverUrl,String User, String PW){ + virtuoso_server_url = serverUrl; + VIRTUOSO_PW = PW; + VIRTUOSO_USER = User; + + try { + th = TripleStoreHandler.getInstance(virtuoso_server_url, VIRTUOSO_USER, VIRTUOSO_PW); + //th = new TripleStoreHandler(virtuoso_server_url, VIRTUOSO_USER, VIRTUOSO_PW); + } catch (TripleStoreHandlerException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + mh = MetaDataHandler.getInstance(); + } + /** + * Hole alle Properties eines Instance wie definiert in OWL. + * @param instance + * @return + */ + private HashMap getProperties(String instance, List NSFilter){ + RepositoryResult stmts; + HashMap retMap = new HashMap(); + try { + stmts= th.getStatements(instance, "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", null); + } catch (RepositoryException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + return null; + } + try { + while(stmts.hasNext()){ + Statement stmt = stmts.next(); + addPropsOfType(retMap,stmt.getObject().stringValue(),instance, NSFilter); + } + } catch (RepositoryException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + return null; + } + + + return retMap; + } + private void addPropsOfType(HashMap retMap, + String cls, String instance, List NSfilter) { + +// Set props = mh.getAssociatedPropsForClass(cls); +// Iterator propsIt = props.iterator(); +// while (propsIt.hasNext()){ +// Object prop = propsIt.next(); +// +// +// } + Collection props = mh.getAssociatedPropsForClass(cls); + + // filter namespaces + if (NSfilter!=null){ + + Object[] propsCopy = props.toArray(); + for (Object prop:propsCopy){ + if (DefaultRDFProperty.class.isInstance(prop)){ + DefaultRDFProperty rdfProp = (DefaultRDFProperty)prop; + rl.debug(rdfProp.getNamespace()); + if (!NSfilter.contains(rdfProp.getNamespace())){ // nicht im filter + props.remove(prop); + } + } + } + } + + Map newProps; + try { + newProps = th.getJenaRDFValues(props, instance, mh.getOwlModel(),true); + } catch (RepositoryException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + return; + } + + retMap.putAll(newProps); + + + } + + @Post + public Representation postHTML(Representation entity){ + User user = handleBasicAuthentification(entity); + if (user==null){ + setStatus(Status.CLIENT_ERROR_UNAUTHORIZED); + return null; + } + + Form form = new Form(entity); + + String id = form.getFirstValue("id"); + if (id==null){ + setStatus(Status.CLIENT_ERROR_BAD_REQUEST); + return new StringRepresentation("Parameter ID missing"); + } + + String type = form.getFirstValue("type"); + if (type==null){ + setStatus(Status.CLIENT_ERROR_BAD_REQUEST); + return new StringRepresentation("Parameter type missing"); + } + + + ArrayList quads = new ArrayList(); + ArrayList deleteQuads = new ArrayList(); + Map formMap = form.getValuesMap(); + for (String key: formMap.keySet()){ + if (isDataTypeProperty(key,type)){ + String value=formMap.get(key); + + //remove white space + value=StringUtils.stripEnd(value, null); + value=StringUtils.stripStart(value, null); + + if (value!=null && !value.equals("")){ //not empty + deleteQuads.add(new LiteralQuadruple(id, key, null, editGraph)); + quads.add(new LiteralQuadruple(id, key, formMap.get(key), editGraph)); + } + } + } + try { + th.remove(deleteQuads); + th.write(quads); + } catch (RepositoryException e) { + setStatus(Status.SERVER_ERROR_INTERNAL); + e.printStackTrace(); + return null; + } catch (TripleStoreHandlerException e) { + setStatus(Status.SERVER_ERROR_INTERNAL); + e.printStackTrace(); + return null; + } + + return new StringRepresentation("written"); + + } + + /** + * Checks if the + * @param key + * @param value + * @return + */ + private boolean isDataTypeProperty(String key,String type) { + + + Collection props = mh.getAssociatedPropsForClass(type); + + + Object[] propsCopy = props.toArray(); + for (Object prop:propsCopy){ + if (DefaultRDFProperty.class.isInstance(prop)){ + DefaultRDFProperty rdfProp = (DefaultRDFProperty)prop; + rl.debug(rdfProp.getNamespace()); + if (rdfProp.getName().equals(key)){ + rl.debug(rdfProp); + return true; + } + } + } + return false; + } + + + @Get("html") + public Representation getHTML(Representation entity){ + Form form = getRequest().getResourceRef().getQueryAsForm(); + + + String id =form.getValuesMap().get("id"); + try { + id = URLDecoder.decode(id, "utf-8"); + } catch (UnsupportedEncodingException e) { + e.printStackTrace(); + e.printStackTrace(); + setStatus(Status.SERVER_ERROR_INTERNAL, "REPOSITORY ERROR"); + return new StringRepresentation( + "Unsupported encoding", + MediaType.TEXT_HTML); + + } + id=StringUtils.stripEnd(id, null); + id=StringUtils.stripStart(id, null); + + ArrayList NSFilter = new ArrayList(); + NSFilter.add("http://xmlns.com/foaf/0.1/"); // only foaf + HashMap props = getProperties(id, NSFilter); + + + ArrayList NSFilterRDF = new ArrayList(); + NSFilterRDF.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#"); // only foaf + HashMap propsRDF = getProperties(id, NSFilterRDF); + + String RDFtype = ((DefaultCls)(propsRDF.get("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"))).getName(); + + + String retString="
"; + retString+=String.format("", id); + retString+=String.format("", RDFtype); + for (String prop: props.keySet()){ + + retString+=String.format("
%s
", + prop,prop,String.valueOf(props.get(prop))); + } + + retString+=""; + retString+="
"; + return new StringRepresentation(retString,MediaType.TEXT_HTML); + + } + + + private User handleBasicAuthentification(Representation entity) { + RestServer restServer = (RestServer) getApplication(); + if (!restServer.authenticate(getRequest(), getResponse())) { + // Not authenticated + return null; + } + + ClientInfo ci = getRequest().getClientInfo(); + rl.debug(ci); + return getRequest().getClientInfo().getUser(); + + } + + public static void main(String args[]) { + Logger.getRootLogger().setLevel(Level.DEBUG); + Editor ed = new Editor("jdbc:virtuoso://virtuoso.mpiwg-berlin.mpg.de:1111","dba","wa55er"); + ArrayList NSFilter = new ArrayList(); + NSFilter.add("http://xmlns.com/foaf/0.1/"); // only foaf + HashMap props = ed.getProperties("http://ontologies.mpiwg-berlin.mpg.de/tempObjects/person/370868",NSFilter); + System.out.println(props); + + } +}