gerrit.simantics Code Review - simantics/platform.git/blob

   1 /*******************************************************************************
   2  * Copyright (c) 2012, 2017 Association for Decentralized Information Management
   3  * in Industry THTH ry.
   4  * All rights reserved. This program and the accompanying materials
   5  * are made available under the terms of the Eclipse Public License v1.0
   6  * which accompanies this distribution, and is available at
   7  * http://www.eclipse.org/legal/epl-v10.html
   8  *
   9  * Contributors:
  10  *     VTT Technical Research Centre of Finland - initial API and implementation
  11  *     Semantum Oy - e.g. #7016
  12  *******************************************************************************/
  13 package org.simantics.graph.db;
  14
  15 import java.io.DataInput;
  16 import java.io.IOException;
  17 import java.io.InputStream;
  18 import java.util.ArrayList;
  19 import java.util.Collections;
  20 import java.util.HashMap;
  21 import java.util.HashSet;
  22 import java.util.Map;
  23 import java.util.Set;
  24 import java.util.TreeMap;
  25
  26 import org.simantics.databoard.Bindings;
  27 import org.simantics.databoard.adapter.AdaptException;
  28 import org.simantics.databoard.binding.Binding;
  29 import org.simantics.databoard.binding.mutable.Variant;
  30 import org.simantics.databoard.serialization.Serializer;
  31 import org.simantics.databoard.type.Datatype;
  32 import org.simantics.databoard.util.URIStringUtils;
  33 import org.simantics.db.ReadGraph;
  34 import org.simantics.db.Resource;
  35 import org.simantics.db.Session;
  36 import org.simantics.db.VirtualGraph;
  37 import org.simantics.db.WriteOnlyGraph;
  38 import org.simantics.db.common.WriteBindings;
  39 import org.simantics.db.common.procedure.adapter.TransientCacheAsyncListener;
  40 import org.simantics.db.common.request.PossibleIndexRoot;
  41 import org.simantics.db.common.uri.UnescapedChildMapOfResource;
  42 import org.simantics.db.common.utils.Logger;
  43 import org.simantics.db.exception.DatabaseException;
  44 import org.simantics.db.service.ClusterBuilder2;
  45 import org.simantics.db.service.ClusterBuilderFactory;
  46 import org.simantics.db.service.ClusteringSupport;
  47 import org.simantics.db.service.SerialisationSupport;
  48 import org.simantics.db.service.XSupport;
  49 import org.simantics.graph.db.TransferableGraphSource.TransferableGraphSourceProcedure;
  50 import org.simantics.graph.db.TransferableGraphSource.TransferableGraphSourceValueProcedure;
  51 import org.simantics.graph.representation.Extensions;
  52 import org.simantics.graph.representation.External;
  53 import org.simantics.graph.representation.Identity;
  54 import org.simantics.graph.representation.IdentityDefinition;
  55 import org.simantics.graph.representation.Internal;
  56 import org.simantics.graph.representation.Optional;
  57 import org.simantics.graph.representation.Root;
  58 import org.simantics.graph.representation.TransferableGraphUtils;
  59 import org.simantics.graph.utils.TGResourceUtil;
  60 import org.simantics.graph.utils.TGResourceUtil.LongAdapter;
  61 import org.simantics.utils.datastructures.Pair;
  62 import org.slf4j.LoggerFactory;
  63
  64 import gnu.trove.map.TIntObjectMap;
  65 import gnu.trove.map.hash.TIntObjectHashMap;
  66
  67 public class StreamingTransferableGraphImportProcess implements TransferableGraphImporter {
  68
  69         private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(StreamingTransferableGraphImportProcess.class);
  70
  71         Resource indexRoot;
  72         TransferableGraphSource tg;
  73         VirtualGraph vg;
  74         IImportAdvisor2 advisor;
  75         TGStatusMonitor monitor;
  76         ClusterBuilder2 builder;
  77         final TGResourceUtil resourceUtil = new TGResourceUtil();
  78
  79         int[] handles;
  80
  81         Map<String,Integer> allMissingExternals = new HashMap<>();
  82         Set<String> missingExternals = new HashSet<>();
  83         Map<String,Resource> resolvedParents = new HashMap<>();
  84         TIntObjectHashMap<Resource> existingInternalMap = new TIntObjectHashMap<>();
  85
  86         int resourceCount;
  87         Identity[] identities;
  88         TreeMap<String, Variant> extensions;
  89
  90         // Builtins
  91         Resource RootLibrary;
  92         Resource String;
  93         Resource ExternalEntity;
  94         Resource Library;
  95
  96         Resource InstanceOf;
  97         Resource ConsistsOf;
  98         Resource PartOf;
  99         Resource HasName;
 100         Resource NameOf;
 101
 102         public StreamingTransferableGraphImportProcess(Session session, VirtualGraph vg, TransferableGraphSource tg, IImportAdvisor2 advisor) {
 103                 this(session, vg, tg, advisor, null);
 104         }
 105
 106         public StreamingTransferableGraphImportProcess(Session session, VirtualGraph vg, TransferableGraphSource tg, IImportAdvisor2 advisor, TGStatusMonitor monitor) {
 107                 this.tg = tg;
 108                 this.vg = vg;
 109                 this.advisor = advisor;
 110                 this.monitor = monitor;
 111         }
 112
 113         private int updatePercentage(int percentage, int done, int total) {
 114                 if (monitor != null && (done & 63) == 0) {
 115                         int current = 100*done / total;
 116                         if (current > percentage) {
 117                                 percentage = current;
 118                                 monitor.status(percentage);
 119                         }
 120                 }
 121                 return percentage;
 122         }
 123
 124         public void readIdentities(ReadGraph g) throws Exception {
 125                 extensions = tg.getExtensions();
 126                 resourceCount = tg.getResourceCount();
 127                 identities = new Identity[tg.getIdentityCount()];
 128                 tg.forIdentities(g, new TransferableGraphSourceProcedure<Identity>() {
 129
 130                         int counter = 0;
 131
 132                         @Override
 133                         public void execute(Identity value) throws Exception {
 134                                 identities[counter++] = value;
 135                         }
 136                 });
 137         }
 138
 139         public void findBuiltins(WriteOnlyGraph g) throws DatabaseException {
 140                 RootLibrary = g.getBuiltin("http:/");
 141                 String = g.getBuiltin(CoreInitialization.LAYER0 + "String");
 142                 Library = g.getBuiltin(CoreInitialization.LAYER0 + "Library");
 143                 InstanceOf = g.getBuiltin(CoreInitialization.LAYER0 + "InstanceOf");
 144                 ConsistsOf = g.getBuiltin(CoreInitialization.LAYER0 + "ConsistsOf");
 145                 PartOf = g.getBuiltin(CoreInitialization.LAYER0 + "PartOf");
 146                 HasName = g.getBuiltin(CoreInitialization.LAYER0 + "HasName");
 147                 NameOf = g.getBuiltin(CoreInitialization.LAYER0 + "NameOf");
 148                 ExternalEntity = g.getBuiltin(CoreInitialization.LAYER0 + "ExternalEntity");
 149         }
 150
 151         public void findBuiltins(ReadGraph g) throws DatabaseException {
 152                 RootLibrary = g.getBuiltin("http:/");
 153                 String = g.getBuiltin(CoreInitialization.LAYER0 + "String");
 154                 Library = g.getBuiltin(CoreInitialization.LAYER0 + "Library");
 155                 InstanceOf = g.getBuiltin(CoreInitialization.LAYER0 + "InstanceOf");
 156                 ConsistsOf = g.getBuiltin(CoreInitialization.LAYER0 + "ConsistsOf");
 157                 PartOf = g.getBuiltin(CoreInitialization.LAYER0 + "PartOf");
 158                 HasName = g.getBuiltin(CoreInitialization.LAYER0 + "HasName");
 159                 NameOf = g.getBuiltin(CoreInitialization.LAYER0 + "NameOf");
 160                 ExternalEntity = g.getBuiltin(CoreInitialization.LAYER0 + "ExternalEntity");
 161         }
 162
 163         void addMissing(int handleIndex, String external) {
 164                 allMissingExternals.put(external, handleIndex);
 165                 Set<String> removals = new HashSet<>();
 166                 for(String ext : missingExternals) if(ext.startsWith(external + "/")) return;
 167                 for(String ext : missingExternals) if(external.startsWith(ext + "/")) removals.add(ext);
 168                 missingExternals.removeAll(removals);
 169                 missingExternals.add(external);
 170         }
 171
 172         void prepare(ReadGraph graph) throws Exception {
 173
 174                 Resource target = advisor.getTarget();
 175                 if(target != null)
 176                         indexRoot = graph.syncRequest(new PossibleIndexRoot(target));
 177
 178                 findBuiltins(graph);
 179                 readIdentities(graph);
 180
 181 //              System.err.println("ext: " + extensions);
 182 //              System.err.println("rc: " + resourceCount);
 183 //              System.err.println("ic: " + identities.length);
 184
 185                 ClusterBuilderFactory factory = graph.getService(ClusterBuilderFactory.class);
 186                 ClusterBuilder2 builder = factory.create(vg, false);
 187
 188                 this.handles = new int[resourceCount];
 189                 TIntObjectMap<Identity> identityMap = TransferableGraphUtils.mapIdentities(identities);
 190
 191                 // We must process roots first, because internal identifiers depend on them.
 192                 for(Identity identity : identities) {
 193                         IdentityDefinition definition = identity.definition;
 194                         if (definition instanceof Root) {
 195                                 Root root = (Root) definition;
 196                                 if (root.name.equals(""))
 197                                         handles[identity.resource] = builder.handle(RootLibrary);
 198                                 else {
 199                                         Resource existing = advisor.analyzeRoot(graph, root);
 200                                         if (existing != null)
 201                                                 handles[identity.resource] = builder.handle(existing);
 202                                 }
 203                         }
 204                 }
 205
 206                 for(Identity identity : identities) {
 207                         IdentityDefinition definition = identity.definition;
 208                         if(definition instanceof External) {
 209                                 External def = (External)definition;
 210                                 if(def.parent == -1) {
 211                                     handles[identity.resource] = builder.handle(RootLibrary);
 212                                 } else {
 213                                         if("@inverse".equals(def.name)) {
 214                                                 int parent = handles[def.parent];
 215                                                 int child = builder.handle(graph.getInverse(builder.resource(parent)));
 216                                                 handles[identity.resource] = child;
 217                                         } else {
 218                                                 int handle = handles[def.parent];
 219                                                 Resource parent = handle != 0 ? builder.resource(handle) : null;
 220                                                 // TODO: escape should be removed when names become well-behaving
 221                                                 if(parent != null) {
 222                                                         resolvedParents.put(graph.getURI(parent), parent);
 223                                                     Map<String,Resource> childMap = graph
 224                                             .syncRequest(new UnescapedChildMapOfResource(parent),
 225                                                     TransientCacheAsyncListener.instance());
 226                                                         Resource child = childMap.get(def.name);
 227                                                         if(child == null) {
 228                                                                 addMissing(identity.resource, graph.getURI(parent) + "/" + URIStringUtils.escape(def.name));
 229                                                         } else {
 230                                                                 handles[identity.resource] = builder.handle(child);
 231                                                         }
 232                                                 } else {
 233                                                     addMissing(identity.resource, TransferableGraphUtils.getURI(resourceCount, identityMap, def.parent) + "/" + URIStringUtils.escape(def.name));
 234                                                 }
 235                                         }
 236                                 }
 237                         }
 238                         else if(definition instanceof Internal) {
 239                                 String uri = TransferableGraphUtils.getURI(resourceCount, identityMap, identity.resource);
 240                                 Resource existing = graph.getPossibleResource(uri);
 241                                 if(existing != null) {
 242                                         existingInternalMap.put(identity.resource, existing);
 243                                 }
 244                         }
 245                         else if(definition instanceof Optional) {
 246                                 External def = (External)definition;
 247                                 Resource parent = builder.resource(handles[def.parent]);
 248                                 if(parent != null)
 249                                         handles[identity.resource] = builder.handle(graph.syncRequest(new UnescapedChildMapOfResource(parent)).get(def.name));
 250                         }
 251                 }
 252
 253                 if (!missingExternals.isEmpty() && failOnMissingEntities())
 254                         throw new MissingDependencyException(this);
 255         }
 256
 257         private boolean failOnMissingEntities() {
 258                 return "true".equalsIgnoreCase(
 259                                 System.getProperty(
 260                                                 "org.simantics.tg.import.failOnMissingEntities",
 261                                                 "false") );
 262         }
 263
 264         @Override
 265         public Resource createChild(WriteOnlyGraph graph, Resource parent, Resource child, String name) throws DatabaseException {
 266                 //System.err.println("child " + parent + " - " + child + " = " + name);
 267             if(child == null) child = graph.newResource();
 268                 Resource nameResource = graph.newResource();
 269                 graph.claim(nameResource, InstanceOf, null, String);
 270                 graph.claimValue(nameResource, name, WriteBindings.STRING);
 271                 graph.claim(child, HasName, NameOf, nameResource);
 272                 graph.claim(parent,  ConsistsOf, PartOf, child);
 273                 return child;
 274         }
 275
 276         int[] getClustering() {
 277                 if (vg != null)
 278                         return null;
 279                 Variant v = extensions.get(Extensions.CLUSTERING);
 280                 if(v == null) return null;
 281                 try {
 282                         return (int[])v.getValue(Bindings.INT_ARRAY);
 283                 } catch (AdaptException e) {
 284                         Logger.defaultLogError(e);
 285                         return null;
 286                 }
 287         }
 288
 289         int[] getClusterSets() {
 290                 if (vg != null)
 291                         return null;
 292                 Variant v = extensions.get(Extensions.CLUSTER_SETS);
 293                 if(v == null) return null;
 294                 try {
 295                         return (int[])v.getValue(Bindings.INT_ARRAY);
 296                 } catch (AdaptException e) {
 297                         Logger.defaultLogError(e);
 298                         return null;
 299                 }
 300         }
 301
 302         boolean needTranslation(Datatype type) {
 303             return resourceUtil.mayHaveResource(type);
 304         }
 305
 306         void findClusterSet(WriteOnlyGraph graph, Resource rootLibrary, int[] clustering, int[] clusterSets, long[] clusters, int id) throws DatabaseException {
 307                 ClusteringSupport support = graph.getService(ClusteringSupport.class);
 308                 if(id == Extensions.ROOT_LIBRARY_CLUSTER_SET || id == Extensions.INDEX_ROOT_CLUSTER_SET) return;
 309                 Resource indexRootClusterSetResource = rootLibrary;
 310                 if(indexRoot != null && support.isClusterSet(indexRoot)) {
 311                         indexRootClusterSetResource = indexRoot;
 312                 } else {
 313                         graph.setClusterSet4NewResource(rootLibrary);
 314                         graph.flushCluster();
 315                 }
 316                 int indexRootCsHandle = builder.handle(indexRootClusterSetResource);
 317                 for(int pos=0,index=0;index<clustering.length;index++) {
 318                         pos += clustering[index];
 319                         if(id < pos) {
 320                                 int cs = clusterSets[index];
 321                                 if(handles[id] == 0) {
 322                                         int csHandle = 0;
 323                                         if(cs == Extensions.ROOT_LIBRARY_CLUSTER_SET) csHandle = builder.handle(rootLibrary);
 324                                         else if(cs == Extensions.INDEX_ROOT_CLUSTER_SET) {
 325                                                 if(indexRoot == null) throw new DatabaseException("No index root was available in TG import.");
 326                                                 csHandle = indexRootCsHandle;
 327                                         }
 328                                         else {
 329                                                 findClusterSet(graph, rootLibrary, clustering, clusterSets, clusters, cs);
 330                                                 csHandle = handles[cs];
 331                                         }
 332
 333                                         if(clusters[index] != 0)
 334                                                 builder.selectCluster(clusters[index]);
 335                                         else if(cs >= 0)
 336                                                 builder.newCluster(csHandle);
 337
 338                                         handles[id] = builder.newResource(csHandle);
 339                                         clusters[index] = support.getCluster(builder.resource(handles[id]));
 340
 341                                         builder.createClusterSet(handles[id]);
 342                                 }
 343                                 return;
 344                         }
 345                 }
 346         }
 347
 348         void createMissing(final WriteOnlyGraph graph) throws Exception {
 349
 350                 if(allMissingExternals.isEmpty()) return;
 351
 352                 XSupport xs = graph.getService(XSupport.class);
 353                 Pair<Boolean,Boolean> serviceMode = xs.getServiceMode();
 354                 xs.setServiceMode(true, false);
 355                 try {
 356                         ArrayList<String> missing = new ArrayList<>(allMissingExternals.keySet());
 357                         Collections.sort(missing);
 358                         for(String uri : missing) {
 359                                 String[] parts = URIStringUtils.splitURI(uri);
 360                                 // URIStringUtils.splitURI returns root URI in non-standard format, so fix it manually as a workaround
 361                                 if (parts[0].equals("http://")) {
 362                                         parts[0] = "http:/";
 363                                 }
 364
 365                                 Resource parent = resolvedParents.get(parts[0]);
 366                                 // TODO: proper exception message
 367                                 if(parent == null) {
 368                                         throw new IllegalStateException("Missing URI: " + uri);
 369                                 }
 370
 371                                 Resource childResource = graph.newResource();
 372                                 graph.claim(childResource, InstanceOf, null, ExternalEntity);
 373
 374                                 Resource nameResource = graph.newResource();
 375                                 graph.claim(nameResource, InstanceOf, null, String);
 376                                 graph.claimValue(nameResource, URIStringUtils.unescape(parts[1]), WriteBindings.STRING);
 377                                 graph.claim(childResource, HasName, NameOf, nameResource);
 378
 379                                 graph.claim(parent, ConsistsOf, PartOf, childResource);
 380
 381                                 resolvedParents.put(uri, childResource);
 382
 383                                 handles[allMissingExternals.get(uri)] = builder.handle(childResource);
 384                         }
 385                 } finally {
 386                         xs.setServiceMode(serviceMode.first, serviceMode.second);
 387                 }
 388         }
 389
 390         void write(final WriteOnlyGraph graph) throws Exception {
 391
 392         final SerialisationSupport ss = graph.getService(SerialisationSupport.class);
 393
 394         ClusterBuilderFactory factory = graph.getService(ClusterBuilderFactory.class);
 395         if(advisor instanceof IImportAdvisor2) {
 396             boolean allowImmutable = ((IImportAdvisor2)advisor).allowImmutableModifications();
 397             builder = factory.create(vg, allowImmutable);
 398         } else {
 399             builder = factory.create(vg, false);
 400         }
 401
 402         createMissing(graph);
 403
 404                 final int[] handles = this.handles;
 405
 406                 int[] clustering = getClustering();
 407                 if(clustering != null) {
 408
 409                         int[] clusterSets = getClusterSets();
 410                         if(clusterSets != null) {
 411
 412                                 assert(clustering.length == clusterSets.length);
 413
 414                                 long[] clusters = new long[clustering.length];
 415
 416                                 // Create clustering
 417                                 for(int i=0;i<clusterSets.length;i++) {
 418                                         findClusterSet(graph, graph.getRootLibrary(), clustering, clusterSets, clusters, clusterSets[i]);
 419                                 }
 420
 421                                 // Then create all resources
 422                                 int i=0;
 423                             for(int j=0;j<clustering.length;j++) {
 424                                 int c = clustering[j];
 425                                 int s = clusterSets[j];
 426                                 int setHandle = 0;
 427                                         if(s == Extensions.ROOT_LIBRARY_CLUSTER_SET)
 428                                                 setHandle = builder.handle(graph.getRootLibrary());
 429                                         else if(s == Extensions.INDEX_ROOT_CLUSTER_SET) {
 430                                                 if(indexRoot == null) throw new DatabaseException("No index root was available in TG import.");
 431                                                 setHandle = builder.handle(indexRoot);
 432                                         }
 433                                         else setHandle = handles[s];
 434                                         // Preserve clustering only for internal resources
 435                                         if(clusters[j] != 0)
 436                                                 builder.selectCluster(clusters[j]);
 437                                         else if(s >= 0)
 438                                                 builder.newCluster(setHandle);
 439                                         for(int r=0;r<c;r++, i++)
 440                                                 if(handles[i] == 0) handles[i] = builder.newResource();
 441                                 }
 442
 443                                 for(;i<handles.length;++i)
 444                                         if(handles[i] == 0) handles[i] = builder.newResource();
 445
 446                         } else {
 447
 448                         int i = 0;
 449                                 for(int c : clustering) {
 450                                         builder.newCluster();
 451                                         for(int r=0;r<c;r++, i++)
 452                                                 if(handles[i] == 0) handles[i] = builder.newResource();
 453                                 }
 454
 455                                 for(;i<handles.length;++i)
 456                                         if(handles[i] == 0) handles[i] = builder.newResource();
 457
 458                         }
 459
 460                 } else {
 461
 462                         // Create blank resources
 463                         for(int i=0;i<handles.length;++i)
 464                                 if(handles[i] == 0) handles[i] = builder.newResource();
 465
 466                 }
 467
 468                 // Internal identities
 469                 for(Identity identity : identities) {
 470                         IdentityDefinition definition = identity.definition;
 471 //                      if(handles[identity.resource] != 0)
 472 //                              continue;
 473                         if(definition instanceof External) {
 474                                 // Already done everything
 475                         }
 476                         else if(definition instanceof Internal) {
 477                                 Internal def = (Internal)definition;
 478                                 Resource external = existingInternalMap.get(identity.resource);
 479                                 if(external != null) {
 480                                         handles[identity.resource] = builder.handle(external);
 481                                 } else {
 482                                         if(handles[identity.resource] != 0)
 483                                                 handles[identity.resource] = builder.handle(advisor.createChild(graph, this, builder.resource(handles[def.parent]), builder.resource(handles[identity.resource]), def.name));
 484                                         else
 485                                                 handles[identity.resource] = builder.handle(advisor.createChild(graph, this, builder.resource(handles[def.parent]), null, def.name));
 486                                 }
 487
 488                         }
 489                         else if(definition instanceof Root) {
 490
 491                                 Root root = (Root)definition;
 492                                 if(handles[identity.resource] != 0)
 493                                         handles[identity.resource] = builder.handle(advisor.createRoot(graph, root, builder.resource(handles[identity.resource])));
 494                                 else
 495                                         handles[identity.resource] = builder.handle(advisor.createRoot(graph, root, null));
 496                         }
 497                         else if(definition instanceof Optional) {
 498                                 Optional def = (Optional)definition;
 499                                 if(handles[identity.resource] != 0) {
 500                                         Resource child = advisor.createChild(graph, this, builder.resource(handles[def.parent]), builder.resource(handles[identity.resource]), def.name);
 501                                         graph.claim(child, InstanceOf, null, Library); // ???
 502                                         handles[identity.resource] = builder.handle(child);
 503                                 } else {
 504                                         Resource child = advisor.createChild(graph, this, builder.resource(handles[def.parent]), null, def.name);
 505                                         graph.claim(child, InstanceOf, null, Library); // ???
 506                                         handles[identity.resource] = builder.handle(child);
 507                                 }
 508                         }
 509                 }
 510
 511                 int[] done = { 0 };
 512                 int[] percentage = { 0 };
 513
 514                 int statementCount = tg.getStatementCount();
 515                 tg.forStatements(null, new TransferableGraphSourceProcedure<int[]>() {
 516
 517                         @Override
 518                         public void execute(int[] value) throws Exception {
 519
 520                                 int sub = value[0];
 521                                 int pred = value[1];
 522                                 int inv = value[2];
 523                                 int obj = value[3];
 524
 525                                 int subject = handles[sub];
 526                                 int predicate = handles[pred];
 527                                 int object = handles[obj];
 528
 529                                 builder.addStatement(graph, subject, predicate, object);
 530                                 if(inv >= 0) {
 531                                     int inverse = handles[inv];
 532                                     builder.addStatement(graph, object, inverse, subject);
 533                                 }
 534
 535                                 // Count from 0% -> 50% => total = statementCount*2
 536                                 percentage[0] = updatePercentage(percentage[0], done[0]++, statementCount*2);
 537
 538                         }
 539
 540                 });
 541
 542                 int valueCount = tg.getValueCount();
 543                 done[0] = 0;
 544
 545                 class ValueProcedure extends InputStream implements TransferableGraphSourceValueProcedure {
 546
 547             private TGResourceUtil util = new TGResourceUtil();
 548                     private DataInput source;
 549
 550             @Override
 551             public void execute(int _resource, Datatype type, DataInput stream) throws Exception {
 552
 553                 source = stream;
 554
 555                 //int file = _resource & 0x80000000;
 556                 int resource = _resource & 0x7FFFFFFF;
 557
 558                 Binding binding = Bindings.getBinding(type);
 559                 Serializer s = Bindings.getSerializer(binding);
 560
 561                 builder.beginValue(handles[resource]);
 562                 if(util.mayHaveResource(type)) {
 563                     Object value = s.deserialize(stream);
 564                     util.adaptValue( binding,  value, new LongAdapter() {
 565                                 @Override
 566                                 public long adapt(long in) {
 567                                     try {
 568                                         return ss.getRandomAccessId(handles[(int)in]);
 569                                     } catch (DatabaseException e) {
 570                                         throw new IllegalStateException(e);
 571                                     }
 572                                 }
 573                             });
 574                     byte[] bytes = s.serialize(value);
 575                     for(byte b : bytes) {
 576                         int val = b;
 577                         if(val < 0) val += 256;
 578                         builder.appendValue(val);
 579                     }
 580                 } else {
 581                     s.skip(this);
 582                 }
 583                 builder.endValue();
 584                 work();
 585
 586             }
 587
 588             @Override
 589             public int read() throws IOException {
 590                 int value = source.readUnsignedByte();
 591                 try {
 592                     builder.appendValue(value);
 593                 } catch (DatabaseException e) {
 594                     LOGGER.error("Failed to write value into database", e);
 595                 }
 596                 return value;
 597             }
 598
 599             @Override
 600             public void rawCopy(int resource, int length, DataInput input) throws Exception {
 601                 builder.beginValue(handles[resource]);
 602                 for (int i = 0; i < length; ++i)
 603                     builder.appendValue(input.readUnsignedByte());
 604                 builder.endValue();
 605                 work();
 606             }
 607
 608             private void work() {
 609                 // Count from 50% -> 100% => [valueCount, valueCount*2)
 610                 percentage[0] = updatePercentage(percentage[0], valueCount + done[0]++, valueCount*2);
 611             }
 612                 };
 613
 614                 tg.forValues2(null, new ValueProcedure());
 615
 616                 for(Resource r : existingInternalMap.valueCollection()) {
 617                         try {
 618                                 graph.deny(r, InstanceOf, null, ExternalEntity, null);
 619                         } catch (DatabaseException e) {
 620                                 graph.deny(r, InstanceOf, null, ExternalEntity, vg);
 621                         }
 622                 }
 623
 624         }
 625
 626         @Override
 627         public long[] getResourceIds(SerialisationSupport serializer) throws DatabaseException {
 628                 final int count = handles.length;
 629                 long[] resourceIds = new long[count];
 630                 for(int i=0;i<count;++i)
 631                     resourceIds[i] = serializer.getRandomAccessId(handles[i]);
 632                 return resourceIds;
 633         }
 634 }