bundles/org.simantics.graph/src/org/simantics/graph/representation/PrettyPrintTG.java

   1 package org.simantics.graph.representation;
   2
   3 import java.io.BufferedInputStream;
   4 import java.io.DataInput;
   5 import java.io.DataInputStream;
   6 import java.io.InputStream;
   7 import java.math.BigInteger;
   8 import java.nio.file.Files;
   9 import java.nio.file.Path;
  10 import java.nio.file.Paths;
  11 import java.security.MessageDigest;
  12 import java.security.NoSuchAlgorithmException;
  13 import java.util.ArrayList;
  14 import java.util.Arrays;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.List;
  18 import java.util.Map;
  19 import java.util.Map.Entry;
  20 import java.util.Set;
  21 import java.util.TreeMap;
  22 import java.util.TreeSet;
  23 import java.util.regex.Matcher;
  24 import java.util.regex.Pattern;
  25 import java.util.stream.Collectors;
  26
  27 import org.simantics.databoard.Bindings;
  28 import org.simantics.databoard.binding.Binding;
  29 import org.simantics.databoard.binding.mutable.Variant;
  30 import org.simantics.databoard.container.DataContainers;
  31 import org.simantics.databoard.parser.DataValuePrinter;
  32 import org.simantics.databoard.parser.PrintFormat;
  33 import org.simantics.databoard.parser.repository.DataValueRepository;
  34 import org.slf4j.Logger;
  35 import org.slf4j.LoggerFactory;
  36
  37 import gnu.trove.list.array.TIntArrayList;
  38 import gnu.trove.map.hash.THashMap;
  39 import gnu.trove.map.hash.TIntIntHashMap;
  40 import gnu.trove.map.hash.TIntObjectHashMap;
  41 import gnu.trove.procedure.TIntIntProcedure;
  42 import gnu.trove.set.hash.TLongHashSet;
  43
  44 /**
  45  * @author Antti Villberg
  46  * @since 1.24.0
  47  */
  48 public class PrettyPrintTG {
  49
  50     private static final Logger LOGGER = LoggerFactory.getLogger(PrettyPrintTG.class);
  51
  52     private static final boolean DEBUG = false;
  53
  54     int blankCounter = 0;
  55     int newBlankCounter = 0;
  56     Map<String, String> blankRewrites = new HashMap<>();
  57     MessageDigest m;
  58
  59     private final Pattern versionExtractPattern = Pattern.compile("^.*-(\\d+\\.\\d+)");
  60
  61     final StringBuilder output;
  62     final Map<String, String> ontologies = new HashMap<>(knownOntologies);
  63     final Set<String> referencedOntologies = new TreeSet<>();
  64
  65     private boolean ignoreIdentifiers;
  66
  67     static class ResourceInfo {
  68         final boolean hasURI;
  69         String name;
  70         final int resource;
  71         boolean newResource = false;
  72
  73         int parent;
  74
  75         boolean inlined = false;
  76
  77         // -1 = no owner, -2 = multiple owners
  78
  79         // Set<ResourceInfo> ownedBy
  80         Set<ResourceInfo> ownedBy = new HashSet<>();
  81
  82         // A Map<Integer, Integer> containing information about resource that
  83         // this resource owns and what are the predicates for forming this
  84         // ownership
  85         TIntIntHashMap ownedResourcesWithPredicates = new TIntIntHashMap();
  86
  87         // int owner = -1;
  88         // int ownerPredicate = 0;
  89         String aliasURI = null;
  90         TIntArrayList owned = new TIntArrayList();
  91
  92         // TIntObjectHashMap<TIntHashSet> statements = new
  93         // TIntObjectHashMap<TIntHashSet>();
  94         public ResourceInfo(boolean hasURI, String name, int resource, int parent) {
  95             this.hasURI = hasURI;
  96             this.name = name;
  97             this.resource = resource;
  98             this.parent = parent;
  99         }
 100
 101         @Override
 102         public String toString() {
 103             return name + (aliasURI != null ? " = <" + aliasURI + ">" : "");
 104         }
 105     }
 106
 107     public PrettyPrintTG(StringBuilder b, boolean ignoreIdentifiers) throws NoSuchAlgorithmException {
 108         output = b;
 109         m = MessageDigest.getInstance("SHA-256");
 110         this.ignoreIdentifiers = ignoreIdentifiers;
 111     }
 112
 113     public PrettyPrintTG() throws NoSuchAlgorithmException {
 114         this(new StringBuilder(), false);
 115     }
 116
 117     TreeMap<String, ResourceInfo> orderedInfos = new TreeMap<>();
 118     TIntObjectHashMap<ResourceInfo> infos = new TIntObjectHashMap<>();
 119
 120     String tgNodeName(String name) {
 121         if (name.contains(" "))
 122             return "\"" + name + "\"";
 123         else
 124             return name;
 125     }
 126
 127     ResourceInfo recurseURI(TransferableGraph1 graph, Identity parent, String parentName, int parentId) {
 128         String name = parentName + "." + tgNodeName(TransferableGraphUtils.getName(parent));
 129         ResourceInfo info = new ResourceInfo(true, name, parent.resource, parentId);
 130         orderedInfos.put(name, info);
 131         // infos.put(parent.resource, info);
 132         for (Identity child : TransferableGraphUtils.getChildren(graph, parent)) {
 133             recurseURI(graph, child, name, info.resource);
 134         }
 135         return info;
 136     }
 137
 138     private TreeMap<String, TreeSet<Integer>> sortByPredicateUniqueStatements(TransferableGraph1 graph, int resource) {
 139         TreeMap<String, TreeSet<Integer>> results = new TreeMap<>();
 140         TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource);
 141         for (int i = 0; i < statements.size(); i += 2) {
 142             int predicate = statements.get(i);
 143             String predicateURI = TransferableGraphUtils.getURI(graph, predicate);
 144             TreeSet<Integer> objects = results.get(predicateURI);
 145             if (objects == null) {
 146                 objects = new TreeSet<>();
 147             }
 148             objects.add(statements.get(i + 1));
 149             results.put(predicateURI, objects);
 150         }
 151         return results;
 152     }
 153
 154     void discoverBlank(TransferableGraph1 graph, int resource, TIntArrayList todo) throws Exception {
 155         // TIntArrayList statements =
 156         // TransferableGraphUtils.getStatements(graph, resource);
 157         // for(int i=0;i<statements.size();i+=2) {
 158         for (TreeSet<Integer> objects : sortByPredicateUniqueStatements(graph, resource).values()) {
 159             for (int object : objects) {
 160                 // int object = statements.get(i+1);
 161                 Identity objectId = TransferableGraphUtils.getIdentity(graph, object);
 162                 if (objectId != null) {
 163                     if (objectId.definition instanceof External)
 164                         continue;
 165                 }
 166                 Value value = TransferableGraphUtils.findValue(graph, object);
 167                 if (value != null) {
 168                     infos.put(object, new ResourceInfo(false, printValue(value), object, resource));
 169                     continue;
 170                 }
 171                 ResourceInfo existing = infos.get(object);
 172                 if (existing == null) {
 173
 174                     existing = new ResourceInfo(false, "blank" + blankCounter++, object, resource);
 175
 176                     // System.out.println("created blank" + blankCounter + "
 177                     // with object " + object + " resource " + resource);
 178                     infos.put(object, existing);
 179                     todo.add(object);
 180                 }
 181             }
 182         }
 183     }
 184
 185     private String makeHash(byte[] data) {
 186         m.reset();
 187         m.update(data, 0, data.length);
 188         return new BigInteger(1, m.digest()).toString(16);
 189     }
 190
 191     void discoverOwners(TransferableGraph1 graph, ResourceInfo info) {
 192         log("Discovering owners for {}", info);
 193         int resource = info.resource;
 194         TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource);
 195         for (int i = 0; i < statements.size(); i += 2) {
 196             int predicate = statements.get(i);
 197             int object = statements.get(i + 1);
 198             ResourceInfo existing = infos.get(object);
 199             if (existing != null) {
 200                 // Add all owners here for now and resolve the best owner later
 201
 202                 // Check if predicate is inverse, this just resolves all
 203                 // predicates to be inverse with ending "Inverse"..
 204                 String predicateUri = rewritePredicateURI(graph, predicate);
 205                 if (!predicateUri.endsWith("Inverse") && !predicateUri.endsWith("Of")) {
 206                     existing.ownedResourcesWithPredicates.put(resource, predicate);
 207                     // if (predicateUri.endsWith("Of")) {
 208                     // System.out.println("asd");
 209                     // } else {
 210                     existing.ownedBy.add(info);
 211                     log("    {} owns {} with {}", existing, info, predicateUri);
 212                     // }
 213                 } else {
 214                     // System.out.println("asd");
 215                 }
 216             }
 217         }
 218     }
 219
 220     DataValueRepository repo = new DataValueRepository();
 221     DataValuePrinter printer = new DataValuePrinter(null, repo);
 222
 223     String printValue(Value value) throws Exception {
 224         StringBuilder sb = new StringBuilder();
 225         printer.setFormat(PrintFormat.SINGLE_LINE);
 226         printer.setOutput(sb);
 227
 228         Variant variant = value.value;
 229         printer.print(variant.getBinding(), variant.getValue());
 230         String formattedOutput = sb.toString();
 231         if (formattedOutput.length() > 100) {
 232             // Ok, value too long, lets calculate a hash for it and store first
 233             // 100 chars as comment
 234             byte[] data = Bindings.getSerializerUnchecked(variant.getBinding()).serialize(variant.getValue());
 235             m.reset();
 236             m.update(data, 0, data.length);
 237             String hash = "\"" + new BigInteger(1, m.digest()).toString(16) + "\"";
 238             return hash + " // " + formattedOutput.substring(0, 100) + "..";
 239         } else {
 240             return formattedOutput;
 241         }
 242     }
 243
 244     public static String getExternalURI(TransferableGraph1 tg, External ext) {
 245         String name = ext.name;
 246         if (name.contains(" "))
 247             name = name.replace(" ", "_").replaceAll("@", "_");// name = "\"" +
 248                                                                // name + "\"";
 249         int parentId = ext.parent;
 250         // if(parentId == 0) return ext.name;
 251         // else {
 252         Identity id = TransferableGraphUtils.getIdentity(tg, parentId);
 253         if (id.definition instanceof External) {
 254             return getExternalURI(tg, (External) id.definition) + "/" + name;
 255         } else if (id.definition instanceof Root) {
 256             Root root = (Root) id.definition;
 257             return "http:/" + root.name + "/" + name;
 258         } else {
 259             return null;
 260         }
 261         // }
 262     }
 263
 264     public static String getExternalURI(TransferableGraph1 tg, int resource) {
 265         Identity id = TransferableGraphUtils.getIdentity(tg, resource);
 266         if (id == null)
 267             return null;
 268         if (id.definition instanceof External) {
 269             External ext = (External) id.definition;
 270             return getExternalURI(tg, ext);
 271         }
 272         return null;
 273     }
 274
 275     String rewritePredicateURI(TransferableGraph1 graph, int predicate) {
 276
 277         String uri = getExternalURI(graph, predicate);
 278         if (uri == null) {
 279             ResourceInfo info = infos.get(predicate);
 280             if (info != null)
 281                 return info.name;
 282             return "_";
 283         }
 284
 285         for (String ontology : ontologies.keySet()) {
 286             if (uri.contains(ontology)) {
 287                 String key = ontologies.get(ontology);
 288                 uri = uri.replace(ontology, key);
 289                 referencedOntologies.add(ontology);
 290             }
 291         }
 292
 293         uri = uri.replace("/", ".");
 294
 295         return uri;
 296
 297     }
 298
 299     static void indent(StringBuilder output, int indent) {
 300         for (int i = 0; i < indent; i++)
 301             output.append("  ");
 302     }
 303
 304     String printBlank(TransferableGraph1 graph, String predicateURI2, ResourceInfo info, int indent) {
 305
 306         if (info.hasURI)
 307             return null;
 308
 309         StringBuilder output = new StringBuilder();
 310
 311         String infoName = info.name;
 312         if (infoName.startsWith("blank")) {
 313             infoName = getBlankRewrite(infoName);
 314         }
 315
 316         if (ignoreIdentifiers) {
 317             if (predicateURI2.contains("L0.identifier")) {
 318                 // Do nothing
 319             } else {
 320                 indent(output, indent);
 321                 output.append(predicateURI2 + " " + infoName + "\n");
 322             }
 323         } else {
 324             indent(output, indent);
 325             output.append(predicateURI2 + " " + infoName + "\n");
 326         }
 327
 328         if (info.ownedResourcesWithPredicates.isEmpty()) {
 329             if (DEBUG)
 330                 System.out.print("printBlank");
 331             String uri = printURI(graph, info, false, indent, false);
 332             if (uri != null)
 333                 output.append(uri);
 334         }
 335         // if(info.owner < 0) {
 336         // printURI(graph, info, false, indent);
 337         // }
 338         return output.toString();
 339     }
 340
 341     private String getBlankRewrite(String infoName) {
 342         String rewrite = blankRewrites.get(infoName);
 343         if (rewrite == null) {
 344             rewrite = "rblank" + newBlankCounter++;
 345             if (DEBUG)
 346                 System.out.println("rewrote " + infoName + " to " + rewrite);
 347             blankRewrites.put(infoName, rewrite);
 348         }
 349         return rewrite;
 350         // return infoName;
 351     }
 352
 353     static long longStm(int predicate, int object) {
 354         return ((predicate & 0xffffffffL) << 32) | (object & 0xffffffffL);
 355     }
 356
 357     private void addInlineStatement(TransferableGraph1 graph, Map<String, Set<String>> statements, String predicate,
 358             ResourceInfo objectInfo, int indent) {
 359         Set<String> objects = statements.get(predicate);
 360         if (objects == null) {
 361             objects = new TreeSet<>();
 362             statements.put(predicate, objects);
 363         }
 364         String uri = printURI(graph, objectInfo, false, indent + 1, true);
 365         if (uri != null) {
 366             // TODO: this is not the right place to remove trailing newline
 367             uri = uri.endsWith("\n") ? uri.substring(0, uri.length() - 2) : uri;
 368             objects.add(uri);
 369         }
 370         objectInfo.inlined = true;
 371     }
 372
 373     void addStatement(Map<String, Set<String>> statements, String predicate, String object) {
 374         // TODO: fix this
 375         if (predicate.endsWith("Inverse"))
 376             return;
 377         Set<String> objects = statements.get(predicate);
 378         if (objects == null) {
 379             objects = new TreeSet<>();
 380             statements.put(predicate, objects);
 381         }
 382         objects.add(object);
 383     }
 384
 385     String printURI(TransferableGraph1 graph, ResourceInfo info, boolean requireURI, int indent, boolean inline) {
 386
 387         if (requireURI && !info.hasURI)
 388             return null;
 389
 390         // Check if this ResourceInfo is already inlined with some other
 391         // ResourceInfo
 392         if (info.inlined)
 393             return null;
 394
 395         Map<String, Set<String>> statements = new TreeMap<>();
 396         Identity consistsOf = TransferableGraphUtils.findExternal(graph,
 397                 "http://www.simantics.org/Layer0-1.1/ConsistsOf");
 398         // Identity partOf = TransferableGraphUtils.findExternal(graph,
 399         // "http://www.simantics.org/Layer0-1.1/PartOf");
 400         TLongHashSet processed = new TLongHashSet();
 401         if (DEBUG)
 402             System.out.println("info.owned.size " + info.owned.size() + info.owned);
 403         for (int i = 0; i < info.owned.size(); i += 2) {
 404             int predicate = info.owned.get(i);
 405             int object = info.owned.get(i + 1);
 406             long stmId = longStm(predicate, object);
 407             if (DEBUG)
 408                 System.out.println(
 409                         "  " + stmId + " is already processed as it is owned (" + predicate + " " + object + ")");
 410             processed.add(stmId);
 411         }
 412
 413         TreeMap<String, Integer> predicateURIs = new TreeMap<>();
 414
 415         TIntArrayList rawStatements = TransferableGraphUtils.getStatements(graph, info.resource);
 416         if (DEBUG)
 417             System.out.println(
 418                     "rawStatements size for " + info.name + " : " + rawStatements.size() + " " + rawStatements);
 419         for (int i = 0; i < rawStatements.size(); i += 2) {
 420             int predicate = rawStatements.get(i);
 421             int object = rawStatements.get(i + 1);
 422             long stmId = longStm(predicate, object);
 423             if (!processed.add(stmId)) {
 424                 if (DEBUG)
 425                     System.out.println("  " + stmId + " is already processed (" + (predicate & 0xffffffffL) + " "
 426                             + (object & 0xffffffffL) + ")");
 427                 continue;
 428             }
 429             if (DEBUG)
 430                 System.out.println("   " + stmId + " is currently being processed (" + (predicate & 0xffffffffL) + " "
 431                         + (object & 0xffffffffL) + ")");
 432             // if (partOf.resource == rawStatements.get(i))
 433             // continue;
 434             if (consistsOf.resource == predicate) {
 435                 // if (!info.owned.isEmpty() && !info.name.startsWith("blank"))
 436                 // {
 437                 if (DEBUG)
 438                     System.out.println("  is consistsof " + predicate + " (" + consistsOf.resource + ")");
 439                 continue;
 440                 // } else {
 441                 // // this will be inlined so lets indent
 442                 // indent++;
 443                 // }
 444             }
 445             String predicateURI = rewritePredicateURI(graph, predicate);
 446             predicateURIs.put(predicateURI, object);
 447         }
 448         for (Entry<String, Integer> entry : predicateURIs.entrySet()) {
 449             String predicateURI = entry.getKey();
 450             int object = entry.getValue();
 451
 452             ResourceInfo objectInfo = infos.get(object);
 453             if (objectInfo == null) {
 454                 String objectURI = rewritePredicateURI(graph, object);
 455                 if (DEBUG)
 456                     System.out.println("  adding statement " + predicateURI + " " + objectURI);
 457                 addStatement(statements, predicateURI, objectURI);
 458             } else if (objectInfo.ownedBy.size() == 1 && objectInfo.ownedBy.contains(info)) {
 459                 // inline printing with _
 460                 if (DEBUG)
 461                     System.out.println("  adding inline statement " + predicateURI + " " + objectInfo.name);
 462                 addInlineStatement(graph, statements, predicateURI, objectInfo, indent);
 463             } else {
 464                 String objectName = objectInfo.name;
 465                 if (objectName.startsWith("blank")) {
 466                     objectName = getBlankRewrite(objectName);
 467                 }
 468                 if (DEBUG)
 469                     System.out.println("  adding statement " + predicateURI + " " + objectName);
 470                 addStatement(statements, predicateURI, objectName);
 471             }
 472         }
 473
 474         if (DEBUG)
 475             System.out.println(
 476                     "statements size for " + info.name + " : " + statements.size() + " " + statements.keySet());
 477
 478         StringBuilder output = new StringBuilder();
 479
 480         if (indent == 0 || inline) {
 481             if ("ROOT".equals(info.name)) {
 482                 output.append("ROOT=<http:/>");
 483             } else if (info.aliasURI != null) {
 484                 output.append(info.name + " = <" + info.aliasURI + ">");
 485             } else {
 486                 String infoName = info.name;
 487                 if (infoName.startsWith("blank")) {
 488                     infoName = getBlankRewrite(infoName);
 489                 }
 490                 output.append(inline ? "_" : infoName);
 491             }
 492             Set<String> instanceOfs = statements.get("L0.InstanceOf");
 493             if (instanceOfs != null) {
 494                 for (String instanceOf : instanceOfs) {
 495                     output.append(" : " + instanceOf);
 496                 }
 497             }
 498             Set<String> subrelationOfs = statements.get("L0.SubrelationOf");
 499             if (subrelationOfs != null) {
 500                 for (String subrelationOf : subrelationOfs) {
 501                     output.append(" <R " + subrelationOf);
 502                 }
 503             }
 504             Set<String> inherits = statements.get("L0.Inherits");
 505             if (inherits != null) {
 506                 for (String inherit : inherits) {
 507                     output.append(" <T " + inherit);
 508                 }
 509             }
 510             output.append("\n");
 511         }
 512
 513         if (info.newResource)
 514             output.append("  @L0.new\n");
 515
 516         for (Map.Entry<String, Set<String>> entry : statements.entrySet()) {
 517             String predicate = entry.getKey();
 518             if (ignoreIdentifiers) {
 519                 if (predicate.equals("L0.identifier")) {
 520                     continue;
 521                 }
 522             }
 523             if ("L0.InstanceOf".equals(predicate))
 524                 continue;
 525             if ("L0.SubrelationOf".equals(predicate))
 526                 continue;
 527             if ("L0.Inherits".equals(predicate))
 528                 continue;
 529             if ("L0.PartOf".equals(predicate))
 530                 continue;
 531
 532             // predicates can be blank
 533             if (predicate.startsWith("blan")) {
 534                 predicate = getBlankRewrite(predicate);
 535             }
 536
 537             Set<String> objects = entry.getValue();
 538             indent(output, indent + 1);
 539             if (objects.size() == 1) {
 540                 output.append(predicate + " " + objects.iterator().next() + "\n");
 541             } else {
 542                 output.append(predicate + "\n");
 543                 for (String object : objects) {
 544                     indent(output, indent + 1);
 545                     output.append("  " + object + "\n");
 546                 }
 547             }
 548         }
 549
 550         TreeMap<String, Integer> ownedOrdered = new TreeMap<>();
 551
 552         for (int i = 0; i < info.owned.size(); i += 2) {
 553             String predicateURI = rewritePredicateURI(graph, info.owned.get(i));
 554             ownedOrdered.put(predicateURI, info.owned.get(i + 1));
 555         }
 556
 557         if (DEBUG)
 558             System.out.println(info.name + " : " + ownedOrdered.keySet());
 559
 560         for (Entry<String, Integer> entry : ownedOrdered.entrySet()) {
 561             String predicateURI = entry.getKey();
 562             int owned = entry.getValue();
 563             ResourceInfo ownedInfo = infos.get(owned);
 564
 565             String blank = printBlank(graph, predicateURI, ownedInfo, indent + 1);
 566             if (blank != null) {
 567                 output.append(blank);
 568             }
 569         }
 570
 571         return output.toString();
 572     }
 573
 574     void prettyPrint(Path input, Path output) throws Exception {
 575
 576         System.out.format("Converting exported shared ontology%n\t" + input.toString()
 577                 + "%nto bundle-compatible ontology%n\t" + output.toString());
 578         try (InputStream is = new BufferedInputStream(Files.newInputStream(input), 128 * 1024)) {
 579             DataInput dis = new DataInputStream(is);
 580             org.simantics.databoard.container.DataContainer container = DataContainers.readFile(dis);
 581             Binding binding = TransferableGraph1.BINDING;
 582             TransferableGraph1 graph = (TransferableGraph1) container.content.getValue(binding);
 583             prettyPrint(graph);
 584             Files.write(output, this.output.toString().getBytes());
 585
 586         }
 587
 588     }
 589
 590     static Map<String, String> knownOntologies = new HashMap<>();
 591
 592     static {
 593         knownOntologies.put("http://www.simantics.org/Layer0-1.1", "L0");
 594         knownOntologies.put("http://www.simantics.org/Layer0X-1.1", "L0X");
 595         knownOntologies.put("http://www.simantics.org/Modeling-1.2", "MOD");
 596         knownOntologies.put("http://www.simantics.org/Diagram-2.2", "DIA");
 597         knownOntologies.put("http://www.simantics.org/Structural-1.2", "STR");
 598         knownOntologies.put("http://www.simantics.org/Document-1.2", "DOC");
 599         knownOntologies.put("http://www.simantics.org/Documentation-1.2", "DOCU");
 600         knownOntologies.put("http://www.simantics.org/G2D-1.1", "G2D");
 601         knownOntologies.put("http://www.simantics.org/SelectionView-1.2", "SEL");
 602         knownOntologies.put("http://www.simantics.org/Viewpoint-1.2", "VP");
 603         knownOntologies.put("http://www.simantics.org/Image2-1.2", "IMAGE2");
 604         knownOntologies.put("http://www.simantics.org/GraphFile-0.1", "GRAPHFILE");
 605         knownOntologies.put("http://www.simantics.org/Project-1.2", "PROJECT");
 606         knownOntologies.put("http://www.semantum.fi/Simupedia-1.0", "SIMUPEDIA");
 607         knownOntologies.put("http://www.semantum.fi/SimupediaWorkbench-1.0", "SIMUPEDIA_WORKBENCH");
 608     }
 609
 610     void prettyPrint(TransferableGraph1 graph) throws Exception {
 611         log("Starting prettyPrint for TransferableGraph with {} resources, {} identities, {} statements and {} values",
 612                 graph.resourceCount, graph.identities, graph.statements.length, graph.values.length);
 613
 614         for (Identity id : graph.identities) {
 615             if (id.definition instanceof Internal) {
 616                 Internal internal = (Internal) id.definition;
 617                 Identity parent = TransferableGraphUtils.getIdentity(graph, internal.parent);
 618                 if (parent.definition instanceof External) {
 619                     log("Resolving internal identity {}", id);
 620                     String name = "BASE";
 621                     ResourceInfo info = new ResourceInfo(true, name, id.resource, -1);
 622                     info.aliasURI = TransferableGraphUtils.getURI(graph, id.resource);
 623                     info.newResource = true;
 624                     orderedInfos.put(name, info);
 625                     // infos.put(id.resource, info);
 626                     log("    which parent is external {} and has an aliasURI {}", parent, info.aliasURI);
 627                     for (Identity child : TransferableGraphUtils.getChildren(graph, id)) {
 628                         recurseURI(graph, child, name, info.resource);
 629                     }
 630                     log("    and has {} children", infos.size());
 631                 }
 632             } else if (id.definition instanceof External) {
 633                 External ext = (External) id.definition;
 634                 // Try to detect shared libraries
 635                 if (ext.name.contains("@")) {
 636
 637                     log("Detected an external shared library {}", ext);
 638
 639                     int index = ext.name.indexOf('@');
 640                     String prefix = ext.name.substring(0, index);
 641                     int index2 = ext.name.indexOf('/', index);
 642                     String ontology = index2 == -1 ? ext.name : ext.name.substring(0, index2);
 643                     String uri = TransferableGraphUtils.getURI(graph, id.resource);
 644
 645                     log("    which was resolved as URI={} and prefix={}", uri, prefix);
 646
 647                     ontologies.put(uri, prefix);
 648
 649                 } else if (ext.name.contains("-")) {
 650                     log("Resolving possible ontology {}", ext);
 651                     String uri = TransferableGraphUtils.getURI(graph, id.resource);
 652                     Matcher m = versionExtractPattern.matcher(uri);
 653                     if (m.matches()) {
 654                         if (!ontologies.containsKey(uri)) {
 655                             int index = ext.name.indexOf('-');
 656                             String prefix = ext.name.substring(0, index);
 657                             log("    and it was resolved as URI={} and prefix {}", uri, prefix);
 658                             ontologies.put(uri, prefix);
 659                         }
 660                     }
 661                 }
 662             }
 663         }
 664
 665         // Discover other resources
 666         log("Discovering other resources..");
 667
 668         TIntArrayList todo = new TIntArrayList();
 669         for (ResourceInfo info : orderedInfos.values()) {
 670             todo.add(info.resource);
 671
 672             // put orderedInfos to infos
 673             infos.put(info.resource, info);
 674         }
 675
 676         while (!todo.isEmpty()) {
 677             int resource = todo.removeAt(todo.size() - 1);
 678             discoverBlank(graph, resource, todo);
 679         }
 680         for (ResourceInfo info : infos.valueCollection())
 681             discoverOwners(graph, info);
 682         // for(ResourceInfo info : infos.valueCollection())
 683         // fixInstanceOf(graph, info);
 684
 685         for (ResourceInfo info : infos.valueCollection()) {
 686             // Old implementation
 687             // if (info.owner >= 0) {
 688             // ResourceInfo ownerInfo = infos.get(info.owner);
 689             // System.out.println("originalOwner : " + info.owner + "
 690             // originalPredicate: " + info.ownerPredicate);
 691             // ownerInfo.owned.add(info.ownerPredicate);
 692             // ownerInfo.owned.add(info.resource);
 693             // }
 694
 695             if (!info.ownedResourcesWithPredicates.isEmpty() && info.ownedResourcesWithPredicates.size() == 1) {
 696                 info.ownedResourcesWithPredicates.forEachEntry(new TIntIntProcedure() {
 697
 698                     @Override
 699                     public boolean execute(int owner, int predicate) {
 700                         ResourceInfo ownerInfo = infos.get(owner);
 701                         ownerInfo.owned.add(predicate);
 702                         ownerInfo.owned.add(info.resource);
 703                         return false;
 704                     }
 705                 });
 706             }
 707         }
 708
 709         // Resolve inverses from ownedBy list
 710         for (ResourceInfo info : infos.valueCollection()) {
 711             for (int i = 0; i < info.owned.size(); i += 2) {
 712                 int object = info.owned.get(i + 1);
 713                 ResourceInfo inf = infos.get(object);
 714                 if (inf != null) {
 715                     info.ownedBy.remove(inf);
 716                 }
 717             }
 718         }
 719
 720         Identity routeGraphConn = TransferableGraphUtils.findExternal(graph,
 721                 "http://www.simantics.org/Diagram-2.2/RouteGraphConnection");
 722         Identity instanceOf = TransferableGraphUtils.findExternal(graph,
 723                 "http://www.simantics.org/Layer0-1.1/InstanceOf");
 724         Identity diagramConnetionToConnection = TransferableGraphUtils.findExternal(graph,
 725                 "http://www.simantics.org/Modeling-1.2/DiagramConnectionToConnection");
 726
 727         for (ResourceInfo infoo : infos.valueCollection()) {
 728             Identity elemTo = TransferableGraphUtils.findExternal(graph, "http://www.simantics.org/Modeling-1.2/ElementToComponent");
 729             if (elemTo != null) {
 730                 int elemToComponent = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource, elemTo);
 731                 if (elemToComponent != TransferableGraphUtils.NOT_FOUND) {
 732
 733                     Identity component = TransferableGraphUtils.getIdentity(graph, elemToComponent);
 734                     Identity internal = TransferableGraphUtils.getIdentity(graph, infoo.resource);
 735                     if (internal.definition instanceof Internal && component.definition instanceof Internal) {
 736                         Internal iComponent = (Internal) component.definition;
 737                         infoo.name = infoo.name.substring(0, infoo.name.lastIndexOf(".") + 1) + iComponent.name;
 738                     }
 739                 }
 740             }
 741
 742             if (instanceOf != null) {
 743                 int instOf = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource, instanceOf);
 744                 if (instOf != TransferableGraphUtils.NOT_FOUND && routeGraphConn != null) {
 745                     if (instOf == routeGraphConn.resource) {
 746                         // Found routegraphconnection, change name
 747                         // Lets go to configuration
 748
 749                         int connection = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource,
 750                                 diagramConnetionToConnection);
 751                         if (connection != TransferableGraphUtils.NOT_FOUND) {
 752                             // Gather all inverse statements to construct unique
 753                             // name
 754                             List<String> nameParts = new ArrayList<>();
 755                             TIntArrayList statements = TransferableGraphUtils.getStatements(graph, connection);
 756                             for (int i = 0; i < statements.size(); i += 2) {
 757                                 int predicate = statements.get(i);
 758                                 Identity possibleInverse = TransferableGraphUtils.getIdentity(graph, predicate);
 759                                 if (possibleInverse != null) {
 760                                     int inverseRelation = TransferableGraphUtils.NOT_FOUND;
 761                                     int parentId = TransferableGraphUtils.NOT_FOUND;
 762                                     if (possibleInverse.definition instanceof Internal) {
 763                                         Internal iPossibleInverse = (Internal) possibleInverse.definition;
 764                                         if (iPossibleInverse.name.equals("Inverse")) {
 765                                             inverseRelation = TransferableGraphUtils.getPossibleObject2(graph,
 766                                                     connection, possibleInverse);
 767                                             parentId = iPossibleInverse.parent;
 768                                         } else {
 769                                             log("Unsupported inverse relation found for {} {}", infoo, iPossibleInverse);
 770                                         }
 771                                     } else if (possibleInverse.definition instanceof External) {
 772                                         External ePossibleInverse = (External) possibleInverse.definition;
 773                                         if (ePossibleInverse.name.equals("Inverse")) {
 774                                             inverseRelation = TransferableGraphUtils.getPossibleObject2(graph,
 775                                                     connection, possibleInverse);
 776                                             parentId = ePossibleInverse.parent;
 777                                         } else {
 778                                             log("This external inverse is unsupported for {} {}", infoo, ePossibleInverse);
 779                                         }
 780                                     } else {
 781                                         log("This type of definition is not supported {}", infoo);
 782                                     }
 783                                     if (inverseRelation != TransferableGraphUtils.NOT_FOUND) {
 784                                         // Ok found something
 785                                         Identity object = TransferableGraphUtils.getIdentity(graph, inverseRelation);
 786                                         Identity parent = TransferableGraphUtils.getIdentity(graph, parentId);
 787                                         String objectName, parentName;
 788                                         if (object.definition instanceof Internal) {
 789                                             objectName = ((Internal) object.definition).name;
 790                                         } else if (object.definition instanceof External) {
 791                                             objectName = ((External) object.definition).name;
 792                                         } else {
 793                                             log("This type of definition is not supported {}", infoo);
 794                                             throw new Error("UNSUPPORTED " + infoo);
 795                                         }
 796                                         if (parent.definition instanceof Internal) {
 797                                             parentName = ((Internal) parent.definition).name;
 798                                         } else if (parent.definition instanceof External) {
 799                                             parentName = ((External) parent.definition).name;
 800                                         } else {
 801                                             log("This type of definition is not supported {}", infoo);
 802                                             throw new Error("UNSUPPORTED " + infoo);
 803                                         }
 804                                         String fullName = parentName + "_" + objectName;
 805                                         nameParts.add(fullName);
 806                                     } else {
 807                                         log("No inverse relation found for {}", infoo);
 808                                     }
 809                                 } else {
 810                                     log("Did not find possible inverse relation for {}", infoo);
 811                                 }
 812                             }
 813                             nameParts.sort((o1, o2) -> o1.compareTo(o2));
 814                             String name = "";
 815                             for (String namep : nameParts) {
 816                                 name += namep;
 817                             }
 818                             infoo.name = infoo.name.substring(0, infoo.name.lastIndexOf(".") + 1) + name;
 819                         } else {
 820                             LOGGER.error("Could not find connection for " + infoo + ". Statements of graph below");
 821                             LOGGER.error(Arrays.toString(graph.statements));
 822                             LOGGER.error("Subject -> Predicate : " + infoo.resource + " -> "
 823                                     + diagramConnetionToConnection.resource);
 824                         }
 825                     }
 826                 }
 827             }
 828         }
 829         for (ResourceInfo info : infos.valueCollection()) {
 830             if (info.name.startsWith("blank")) {
 831                 info.name = "blank" + findHash(graph, info);
 832             }
 833         }
 834
 835         TreeMap<String, ResourceInfo> order = new TreeMap<>();
 836         for (ResourceInfo info : infos.valueCollection())
 837             order.put(info.name, info);
 838
 839         for (ResourceInfo info : order.values()) {
 840             if (DEBUG)
 841                 System.out.print("info ");
 842             String uri = printURI(graph, info, true, 0, false);
 843             if (uri != null)
 844                 output.append(uri);
 845         }
 846
 847         TreeMap<String, ResourceInfo> rblanks = new TreeMap<>();
 848
 849         for (ResourceInfo info : order.values()) {
 850             if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) {
 851                 if (DEBUG)
 852                     System.out.print("ownedResources ");
 853                 if (info.name.startsWith("blank")) {
 854                     // These will be printed later
 855                     rblanks.put(getBlankRewrite(info.name), info);
 856                 } else {
 857                     String uri = printURI(graph, info, false, 0, false);
 858                     if (uri != null)
 859                         output.append(uri);
 860                 }
 861             }
 862         }
 863         // Now print blanks in order
 864         for (ResourceInfo info : rblanks.values()) {
 865             if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) {
 866                 if (DEBUG)
 867                     System.out.print("ownedResources ");
 868                 String uri = printURI(graph, info, false, 0, false);
 869                 if (uri != null)
 870                     output.append(uri);
 871             }
 872         }
 873
 874         // for(ResourceInfo info : order.values())
 875         // if(!info.hasURI && info.owner < 0)
 876         // printURI(graph, info, false, 0);
 877
 878         StringBuilder refs = new StringBuilder();
 879         for (String ontology : referencedOntologies) {
 880             String key = ontologies.get(ontology);
 881             refs.append(key + " = <" + ontology + ">\n");
 882         }
 883         if (!referencedOntologies.isEmpty())
 884             refs.append("\n");
 885         output.insert(0, refs.toString());
 886
 887     }
 888
 889     private String calculateHash(TransferableGraph1 graph, ResourceInfo info) {
 890         StringBuilder statementHash = new StringBuilder();
 891         TreeSet<String> parts = new TreeSet<>();
 892         for (int i = 0; i < info.owned.size(); i += 2) {
 893             int predicate = info.owned.get(i);
 894             int object = info.owned.get(i + 1);
 895             // Lets resolve a unique name for this based on the statements this
 896             // one has
 897
 898             String predicatee = rewritePredicateURI(graph, predicate);
 899             ResourceInfo objInfo = infos.get(object);
 900             parts.add(predicatee + "->" + objInfo.name + ";;;");
 901         }
 902         // Remove this from the list
 903         List<ResourceInfo> filtered = info.ownedBy.stream().filter(ri -> !ri.name.startsWith("blank"))
 904                 .collect(Collectors.toList());
 905         for (ResourceInfo ownedBy : filtered) {
 906             parts.add(ownedBy.name);
 907         }
 908         // check parent
 909         ResourceInfo parentInfo = infos.get(info.parent);
 910         if (parentInfo != null && !parentInfo.name.startsWith("blank")) {
 911             parts.add("parent" + parentInfo.name);
 912         } else {
 913             // LOGGER.error("This should not happen");
 914         }
 915         for (String s : parts) {
 916             statementHash.append(s);
 917         }
 918         String hash = makeHash(statementHash.toString().getBytes());
 919         if (DEBUG)
 920             System.out.println(statementHash + " -> " + hash);
 921         return hash;
 922     }
 923
 924     private String findHash(TransferableGraph1 graph, ResourceInfo info) {
 925         if (info.name.startsWith("blank")) {
 926             String hash = hashes.get(info.name);
 927             if (hash == null) {
 928                 String oldName = info.name;
 929                 if (DEBUG)
 930                     System.out.print("calculating hash for " + oldName + " ");
 931                 hash = calculateHash(graph, info);
 932                 if (hashes.put(oldName, hash) != null) {
 933                     System.err.println("!!!!A clash occured for " + info + " with hash " + hash);
 934                 }
 935             }
 936             return hash;
 937         } else {
 938             return info.name;
 939         }
 940     }
 941
 942     private THashMap<String, String> hashes = new THashMap<>();
 943
 944     public static String print(TransferableGraph1 tg, boolean ignoreIdentifiers) throws Exception {
 945         StringBuilder b = new StringBuilder();
 946         new PrettyPrintTG(b, ignoreIdentifiers).prettyPrint(tg);
 947         return b.toString();
 948     }
 949
 950     public static void main(String[] args) throws Exception {
 951         if (args.length < 1) {
 952             System.out.println("Required arguments: <input .sharedOntology file> [<output .tg file>]");
 953         } else if (args.length < 2) {
 954             Path input = Paths.get(args[0]);
 955             Path output = input.getParent().resolve(input.getName(input.getNameCount() - 1) + ".fixed");
 956             new PrettyPrintTG().prettyPrint(input, output);
 957         } else {
 958             new PrettyPrintTG().prettyPrint(Paths.get(args[0]), Paths.get(args[1]));
 959         }
 960     }
 961
 962     private static void log(String string, Object... args) {
 963         if (LOGGER.isDebugEnabled() && DEBUG)
 964             LOGGER.debug(string, args);
 965     }
 966
 967 }