bundles/org.simantics.graph.db/src/org/simantics/graph/db/StreamingTransferableGraphImportProcess.java

   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                 for(Identity identity : identities) {
 192                         IdentityDefinition definition = identity.definition;
 193                         if(definition instanceof External) {
 194                                 External def = (External)definition;
 195                                 if(def.parent == -1) {
 196                                     handles[identity.resource] = builder.handle(RootLibrary);
 197                                 } else {
 198                                         if("@inverse".equals(def.name)) {
 199                                                 int parent = handles[def.parent];
 200                                                 int child = builder.handle(graph.getInverse(builder.resource(parent)));
 201                                                 handles[identity.resource] = child;
 202                                         } else {
 203                                                 int handle = handles[def.parent];
 204                                                 Resource parent = handle != 0 ? builder.resource(handle) : null;
 205                                                 // TODO: escape should be removed when names become well-behaving
 206                                                 if(parent != null) {
 207                                                         resolvedParents.put(graph.getURI(parent), parent);
 208                                                     Map<String,Resource> childMap = graph
 209                                             .syncRequest(new UnescapedChildMapOfResource(parent),
 210                                                     TransientCacheAsyncListener.instance());
 211                                                         Resource child = childMap.get(def.name);
 212                                                         if(child == null) {
 213                                                                 addMissing(identity.resource, graph.getURI(parent) + "/" + URIStringUtils.escape(def.name));
 214                                                         } else {
 215                                                                 handles[identity.resource] = builder.handle(child);
 216                                                         }
 217                                                 } else {
 218                                                     addMissing(identity.resource, TransferableGraphUtils.getURI(resourceCount, identityMap, def.parent) + "/" + URIStringUtils.escape(def.name));
 219                                                 }
 220                                         }
 221                                 }
 222                         }
 223                         else if(definition instanceof Internal) {
 224                                 String uri = TransferableGraphUtils.getURI(resourceCount, identityMap, identity.resource);
 225                                 Resource existing = graph.getPossibleResource(uri);
 226                                 if(existing != null) {
 227                                         existingInternalMap.put(identity.resource, existing);
 228                                 }
 229                         }
 230                         else if(definition instanceof Root) {
 231                                 Root root = (Root)definition;
 232                                 if(root.name.equals(""))
 233                                     handles[identity.resource] = builder.handle(RootLibrary);
 234                                 else  {
 235                                         Resource existing = advisor.analyzeRoot(graph, root);
 236                                         if(existing != null)
 237                                             handles[identity.resource] = builder.handle(existing);
 238                                 }
 239                         }
 240                         else if(definition instanceof Optional) {
 241                                 External def = (External)definition;
 242                                 Resource parent = builder.resource(handles[def.parent]);
 243                                 if(parent != null)
 244                                         handles[identity.resource] = builder.handle(graph.syncRequest(new UnescapedChildMapOfResource(parent)).get(def.name));
 245                         }
 246                 }
 247
 248                 if (!missingExternals.isEmpty() && failOnMissingEntities())
 249                         throw new MissingDependencyException(this);
 250         }
 251
 252         private boolean failOnMissingEntities() {
 253                 return "true".equalsIgnoreCase(
 254                                 System.getProperty(
 255                                                 "org.simantics.tg.import.failOnMissingEntities",
 256                                                 "false") );
 257         }
 258
 259         @Override
 260         public Resource createChild(WriteOnlyGraph graph, Resource parent, Resource child, String name) throws DatabaseException {
 261                 //System.err.println("child " + parent + " - " + child + " = " + name);
 262             if(child == null) child = graph.newResource();
 263                 Resource nameResource = graph.newResource();
 264                 graph.claim(nameResource, InstanceOf, null, String);
 265                 graph.claimValue(nameResource, name, WriteBindings.STRING);
 266                 graph.claim(child, HasName, NameOf, nameResource);
 267                 graph.claim(parent,  ConsistsOf, PartOf, child);
 268                 return child;
 269         }
 270
 271         int[] getClustering() {
 272                 Variant v = extensions.get(Extensions.CLUSTERING);
 273                 if(v == null) return null;
 274                 try {
 275                         return (int[])v.getValue(Bindings.INT_ARRAY);
 276                 } catch (AdaptException e) {
 277                         Logger.defaultLogError(e);
 278                         return null;
 279                 }
 280         }
 281
 282         int[] getClusterSets() {
 283                 Variant v = extensions.get(Extensions.CLUSTER_SETS);
 284                 if(v == null) return null;
 285                 try {
 286                         return (int[])v.getValue(Bindings.INT_ARRAY);
 287                 } catch (AdaptException e) {
 288                         Logger.defaultLogError(e);
 289                         return null;
 290                 }
 291         }
 292
 293         boolean needTranslation(Datatype type) {
 294             return resourceUtil.mayHaveResource(type);
 295         }
 296
 297         void findClusterSet(WriteOnlyGraph graph, Resource rootLibrary, int[] clustering, int[] clusterSets, long[] clusters, int id) throws DatabaseException {
 298                 ClusteringSupport support = graph.getService(ClusteringSupport.class);
 299                 if(id == Extensions.ROOT_LIBRARY_CLUSTER_SET || id == Extensions.INDEX_ROOT_CLUSTER_SET) return;
 300                 Resource indexRootClusterSetResource = rootLibrary;
 301                 if(indexRoot != null && support.isClusterSet(indexRoot)) {
 302                         indexRootClusterSetResource = indexRoot;
 303                 } else {
 304                         graph.setClusterSet4NewResource(rootLibrary);
 305                         graph.flushCluster();
 306                 }
 307                 int indexRootCsHandle = builder.handle(indexRootClusterSetResource);
 308                 for(int pos=0,index=0;index<clustering.length;index++) {
 309                         pos += clustering[index];
 310                         if(id < pos) {
 311                                 int cs = clusterSets[index];
 312                                 if(handles[id] == 0) {
 313                                         int csHandle = 0;
 314                                         if(cs == Extensions.ROOT_LIBRARY_CLUSTER_SET) csHandle = builder.handle(rootLibrary);
 315                                         else if(cs == Extensions.INDEX_ROOT_CLUSTER_SET) {
 316                                                 if(indexRoot == null) throw new DatabaseException("No index root was available in TG import.");
 317                                                 csHandle = indexRootCsHandle;
 318                                         }
 319                                         else {
 320                                                 findClusterSet(graph, rootLibrary, clustering, clusterSets, clusters, cs);
 321                                                 csHandle = handles[cs];
 322                                         }
 323
 324                                         if(clusters[index] != 0)
 325                                                 builder.selectCluster(clusters[index]);
 326                                         else if(cs >= 0)
 327                                                 builder.newCluster(csHandle);
 328
 329                                         handles[id] = builder.newResource(csHandle);
 330                                         clusters[index] = support.getCluster(builder.resource(handles[id]));
 331
 332                                         builder.createClusterSet(handles[id]);
 333                                 }
 334                                 return;
 335                         }
 336                 }
 337         }
 338
 339         void createMissing(final WriteOnlyGraph graph) throws Exception {
 340
 341                 if(allMissingExternals.isEmpty()) return;
 342
 343                 XSupport xs = graph.getService(XSupport.class);
 344                 Pair<Boolean,Boolean> serviceMode = xs.getServiceMode();
 345                 xs.setServiceMode(true, false);
 346                 try {
 347                         ArrayList<String> missing = new ArrayList<>(allMissingExternals.keySet());
 348                         Collections.sort(missing);
 349                         for(String uri : missing) {
 350                                 String[] parts = URIStringUtils.splitURI(uri);
 351                                 // URIStringUtils.splitURI returns root URI in non-standard format, so fix it manually as a workaround
 352                                 if (parts[0].equals("http://")) {
 353                                         parts[0] = "http:/";
 354                                 }
 355
 356                                 Resource parent = resolvedParents.get(parts[0]);
 357                                 // TODO: proper exception message
 358                                 if(parent == null) {
 359                                         throw new IllegalStateException("Missing URI: " + uri);
 360                                 }
 361
 362                                 Resource childResource = graph.newResource();
 363                                 graph.claim(childResource, InstanceOf, null, ExternalEntity);
 364
 365                                 Resource nameResource = graph.newResource();
 366                                 graph.claim(nameResource, InstanceOf, null, String);
 367                                 graph.claimValue(nameResource, URIStringUtils.unescape(parts[1]), WriteBindings.STRING);
 368                                 graph.claim(childResource, HasName, NameOf, nameResource);
 369
 370                                 graph.claim(parent, ConsistsOf, PartOf, childResource);
 371
 372                                 resolvedParents.put(uri, childResource);
 373
 374                                 handles[allMissingExternals.get(uri)] = builder.handle(childResource);
 375                         }
 376                 } finally {
 377                         xs.setServiceMode(serviceMode.first, serviceMode.second);
 378                 }
 379         }
 380
 381         void write(final WriteOnlyGraph graph) throws Exception {
 382
 383         final SerialisationSupport ss = graph.getService(SerialisationSupport.class);
 384
 385         ClusterBuilderFactory factory = graph.getService(ClusterBuilderFactory.class);
 386         if(advisor instanceof IImportAdvisor2) {
 387             boolean allowImmutable = ((IImportAdvisor2)advisor).allowImmutableModifications();
 388             builder = factory.create(vg, allowImmutable);
 389         } else {
 390             builder = factory.create(vg, false);
 391         }
 392
 393         createMissing(graph);
 394
 395                 final int[] handles = this.handles;
 396
 397                 int[] clustering = getClustering();
 398                 if(clustering != null) {
 399
 400                         int[] clusterSets = getClusterSets();
 401                         if(clusterSets != null) {
 402
 403                                 assert(clustering.length == clusterSets.length);
 404
 405                                 long[] clusters = new long[clustering.length];
 406
 407                                 // Create clustering
 408                                 for(int i=0;i<clusterSets.length;i++) {
 409                                         findClusterSet(graph, graph.getRootLibrary(), clustering, clusterSets, clusters, clusterSets[i]);
 410                                 }
 411
 412                                 // Then create all resources
 413                                 int i=0;
 414                             for(int j=0;j<clustering.length;j++) {
 415                                 int c = clustering[j];
 416                                 int s = clusterSets[j];
 417                                 int setHandle = 0;
 418                                         if(s == Extensions.ROOT_LIBRARY_CLUSTER_SET)
 419                                                 setHandle = builder.handle(graph.getRootLibrary());
 420                                         else if(s == Extensions.INDEX_ROOT_CLUSTER_SET) {
 421                                                 if(indexRoot == null) throw new DatabaseException("No index root was available in TG import.");
 422                                                 setHandle = builder.handle(indexRoot);
 423                                         }
 424                                         else setHandle = handles[s];
 425                                         // Preserve clustering only for internal resources
 426                                         if(clusters[j] != 0)
 427                                                 builder.selectCluster(clusters[j]);
 428                                         else if(s >= 0)
 429                                                 builder.newCluster(setHandle);
 430                                         for(int r=0;r<c;r++, i++)
 431                                                 if(handles[i] == 0) handles[i] = builder.newResource();
 432                                 }
 433
 434                                 for(;i<handles.length;++i)
 435                                         if(handles[i] == 0) handles[i] = builder.newResource();
 436
 437                         } else {
 438
 439                         int i = 0;
 440                                 for(int c : clustering) {
 441                                         builder.newCluster();
 442                                         for(int r=0;r<c;r++, i++)
 443                                                 if(handles[i] == 0) handles[i] = builder.newResource();
 444                                 }
 445
 446                                 for(;i<handles.length;++i)
 447                                         if(handles[i] == 0) handles[i] = builder.newResource();
 448
 449                         }
 450
 451                 } else {
 452
 453                         // Create blank resources
 454                         for(int i=0;i<handles.length;++i)
 455                                 if(handles[i] == 0) handles[i] = builder.newResource();
 456
 457                 }
 458
 459                 // Internal identities
 460                 for(Identity identity : identities) {
 461                         IdentityDefinition definition = identity.definition;
 462 //                      if(handles[identity.resource] != 0)
 463 //                              continue;
 464                         if(definition instanceof External) {
 465                                 // Already done everything
 466                         }
 467                         else if(definition instanceof Internal) {
 468                                 Internal def = (Internal)definition;
 469                                 Resource external = existingInternalMap.get(identity.resource);
 470                                 if(external != null) {
 471                                         handles[identity.resource] = builder.handle(external);
 472                                 } else {
 473                                         if(handles[identity.resource] != 0)
 474                                                 handles[identity.resource] = builder.handle(advisor.createChild(graph, this, builder.resource(handles[def.parent]), builder.resource(handles[identity.resource]), def.name));
 475                                         else
 476                                                 handles[identity.resource] = builder.handle(advisor.createChild(graph, this, builder.resource(handles[def.parent]), null, def.name));
 477                                 }
 478
 479                         }
 480                         else if(definition instanceof Root) {
 481
 482                                 Root root = (Root)definition;
 483                                 if(handles[identity.resource] != 0)
 484                                         handles[identity.resource] = builder.handle(advisor.createRoot(graph, root, builder.resource(handles[identity.resource])));
 485                                 else
 486                                         handles[identity.resource] = builder.handle(advisor.createRoot(graph, root, null));
 487                         }
 488                         else if(definition instanceof Optional) {
 489                                 Optional def = (Optional)definition;
 490                                 if(handles[identity.resource] != 0) {
 491                                         Resource child = advisor.createChild(graph, this, builder.resource(handles[def.parent]), builder.resource(handles[identity.resource]), def.name);
 492                                         graph.claim(child, InstanceOf, null, Library); // ???
 493                                         handles[identity.resource] = builder.handle(child);
 494                                 } else {
 495                                         Resource child = advisor.createChild(graph, this, builder.resource(handles[def.parent]), null, def.name);
 496                                         graph.claim(child, InstanceOf, null, Library); // ???
 497                                         handles[identity.resource] = builder.handle(child);
 498                                 }
 499                         }
 500                 }
 501
 502                 int[] done = { 0 };
 503                 int[] percentage = { 0 };
 504
 505                 int statementCount = tg.getStatementCount();
 506                 tg.forStatements(null, new TransferableGraphSourceProcedure<int[]>() {
 507
 508                         @Override
 509                         public void execute(int[] value) throws Exception {
 510
 511                                 int sub = value[0];
 512                                 int pred = value[1];
 513                                 int inv = value[2];
 514                                 int obj = value[3];
 515
 516                                 int subject = handles[sub];
 517                                 int predicate = handles[pred];
 518                                 int object = handles[obj];
 519
 520                                 builder.addStatement(graph, subject, predicate, object);
 521                                 if(inv >= 0) {
 522                                     int inverse = handles[inv];
 523                                     builder.addStatement(graph, object, inverse, subject);
 524                                 }
 525
 526                                 // Count from 0% -> 50% => total = statementCount*2
 527                                 percentage[0] = updatePercentage(percentage[0], done[0]++, statementCount*2);
 528
 529                         }
 530
 531                 });
 532
 533                 int valueCount = tg.getValueCount();
 534                 done[0] = 0;
 535
 536                 class ValueProcedure extends InputStream implements TransferableGraphSourceValueProcedure {
 537
 538             private TGResourceUtil util = new TGResourceUtil();
 539                     private DataInput source;
 540
 541             @Override
 542             public void execute(int _resource, Datatype type, DataInput stream) throws Exception {
 543
 544                 source = stream;
 545
 546                 //int file = _resource & 0x80000000;
 547                 int resource = _resource & 0x7FFFFFFF;
 548
 549                 Binding binding = Bindings.getBinding(type);
 550                 Serializer s = Bindings.getSerializer(binding);
 551
 552                 builder.beginValue(handles[resource]);
 553                 if(util.mayHaveResource(type)) {
 554                     Object value = s.deserialize(stream);
 555                     util.adaptValue( binding,  value, new LongAdapter() {
 556                                 @Override
 557                                 public long adapt(long in) {
 558                                     try {
 559                                         return ss.getRandomAccessId(handles[(int)in]);
 560                                     } catch (DatabaseException e) {
 561                                         throw new IllegalStateException(e);
 562                                     }
 563                                 }
 564                             });
 565                     byte[] bytes = s.serialize(value);
 566                     for(byte b : bytes) {
 567                         int val = b;
 568                         if(val < 0) val += 256;
 569                         builder.appendValue(val);
 570                     }
 571                 } else {
 572                     s.skip(this);
 573                 }
 574                 builder.endValue();
 575                 work();
 576
 577             }
 578
 579             @Override
 580             public int read() throws IOException {
 581                 int value = source.readUnsignedByte();
 582                 try {
 583                     builder.appendValue(value);
 584                 } catch (DatabaseException e) {
 585                     LOGGER.error("Failed to write value into database", e);
 586                 }
 587                 return value;
 588             }
 589
 590             @Override
 591             public void rawCopy(int resource, int length, DataInput input) throws Exception {
 592                 builder.beginValue(handles[resource]);
 593                 for (int i = 0; i < length; ++i)
 594                     builder.appendValue(input.readUnsignedByte());
 595                 builder.endValue();
 596                 work();
 597             }
 598
 599             private void work() {
 600                 // Count from 50% -> 100% => [valueCount, valueCount*2)
 601                 percentage[0] = updatePercentage(percentage[0], valueCount + done[0]++, valueCount*2);
 602             }
 603                 };
 604
 605                 tg.forValues2(null, new ValueProcedure());
 606
 607                 for(Resource r : existingInternalMap.valueCollection()) {
 608                         graph.deny(r, InstanceOf, null, ExternalEntity, null);
 609                 }
 610
 611         }
 612
 613         @Override
 614         public long[] getResourceIds(SerialisationSupport serializer) throws DatabaseException {
 615                 final int count = handles.length;
 616                 long[] resourceIds = new long[count];
 617                 for(int i=0;i<count;++i)
 618                     resourceIds[i] = serializer.getRandomAccessId(handles[i]);
 619                 return resourceIds;
 620         }
 621 }