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.HashMap;
  14 import java.util.HashSet;
  15 import java.util.Map;
  16 import java.util.Set;
  17 import java.util.TreeMap;
  18 import java.util.TreeSet;
  19 import java.util.regex.Matcher;
  20 import java.util.regex.Pattern;
  21
  22 import org.simantics.databoard.Bindings;
  23 import org.simantics.databoard.binding.Binding;
  24 import org.simantics.databoard.binding.mutable.Variant;
  25 import org.simantics.databoard.container.DataContainers;
  26 import org.simantics.databoard.parser.DataValuePrinter;
  27 import org.simantics.databoard.parser.PrintFormat;
  28 import org.simantics.databoard.parser.repository.DataValueRepository;
  29 import org.slf4j.Logger;
  30 import org.slf4j.LoggerFactory;
  31
  32 import gnu.trove.list.array.TIntArrayList;
  33 import gnu.trove.map.hash.TIntIntHashMap;
  34 import gnu.trove.map.hash.TIntObjectHashMap;
  35 import gnu.trove.procedure.TIntIntProcedure;
  36 import gnu.trove.set.hash.TLongHashSet;
  37
  38 /**
  39  * @author Antti Villberg
  40  * @since 1.24.0
  41  */
  42 public class PrettyPrintTG {
  43
  44     private static final Logger LOGGER = LoggerFactory.getLogger(PrettyPrintTG.class);
  45
  46         int blankCounter = 0;
  47         MessageDigest m;
  48
  49         private final Pattern versionExtractPattern = Pattern.compile("^.*-(\\d+\\.\\d+)");
  50
  51         final StringBuilder output;
  52         final Map<String,String> ontologies = new HashMap<>(knownOntologies);
  53         final Set<String> referencedOntologies = new TreeSet<>();
  54
  55         static class ResourceInfo {
  56                 final boolean hasURI;
  57                 final String name;
  58                 final int resource;
  59                 boolean newResource = false;
  60
  61                 int parent;
  62
  63                 boolean inlined = false;
  64
  65                 // -1 = no owner, -2 = multiple owners
  66
  67                 // Set<ResourceInfo> ownedBy
  68                 Set<ResourceInfo> ownedBy = new HashSet<>();
  69
  70                 // A Map<Integer, Integer> containing information about resource that this resource owns and what are the predicates for forming this ownership
  71                 TIntIntHashMap ownedResourcesWithPredicates = new TIntIntHashMap();
  72
  73 //              int owner = -1;
  74 //              int ownerPredicate = 0;
  75                 String aliasURI = null;
  76                 TIntArrayList owned = new TIntArrayList();
  77                 //TIntObjectHashMap<TIntHashSet> statements = new TIntObjectHashMap<TIntHashSet>();
  78                 public ResourceInfo(boolean hasURI, String name, int resource, int parent) {
  79                         this.hasURI = hasURI;
  80                         this.name = name;
  81                         this.resource = resource;
  82                         this.parent = parent;
  83                 }
  84
  85                 @Override
  86                 public String toString() {
  87                     return name + (aliasURI != null ? " = <" + aliasURI + ">" : "");
  88                 }
  89         }
  90
  91         public PrettyPrintTG(StringBuilder b) throws NoSuchAlgorithmException {
  92                 output = b;
  93                 m = MessageDigest.getInstance("SHA-256");
  94         }
  95
  96         public PrettyPrintTG() throws NoSuchAlgorithmException {
  97                 this(new StringBuilder());
  98         }
  99
 100         TIntObjectHashMap<ResourceInfo> infos = new TIntObjectHashMap<>();
 101
 102         String tgNodeName(String name) {
 103                 if(name.contains(" ")) return "\"" + name + "\"";
 104                 else return name;
 105         }
 106
 107         ResourceInfo recurseURI(TransferableGraph1 graph, Identity parent, String parentName, int parentId) {
 108                 String name = parentName + "." + tgNodeName(TransferableGraphUtils.getName(parent));
 109                 ResourceInfo info = new ResourceInfo(true, name, parent.resource, parentId);
 110                 infos.put(parent.resource, info);
 111                 for(Identity child : TransferableGraphUtils.getChildren(graph, parent)) {
 112                         recurseURI(graph, child, name, info.resource);
 113                 }
 114                 return info;
 115         }
 116
 117         void discoverBlank(TransferableGraph1 graph, int resource, TIntArrayList todo) throws Exception {
 118                 TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource);
 119                 for(int i=0;i<statements.size();i+=2) {
 120                         int object = statements.get(i+1);
 121                         Identity objectId = TransferableGraphUtils.getIdentity(graph, object);
 122                         if(objectId != null) {
 123                                 if(objectId.definition instanceof External) continue;
 124                         }
 125                         Value value = TransferableGraphUtils.findValue(graph, object);
 126                         if(value != null) {
 127                                 infos.put(object, new ResourceInfo(false, printValue(value), object, resource));
 128                                 continue;
 129                         }
 130                         ResourceInfo existing = infos.get(object);
 131                         if(existing == null) {
 132                                 existing = new ResourceInfo(false, "blank" + blankCounter++, object, resource);
 133                                 infos.put(object, existing);
 134                                 todo.add(object);
 135                         }
 136                 }
 137         }
 138
 139         void discoverOwners(TransferableGraph1 graph, ResourceInfo info) {
 140             if (LOGGER.isDebugEnabled())
 141                 LOGGER.debug("Discovering owners for " + info);
 142                 int resource = info.resource;
 143                 TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource);
 144                 for(int i=0;i<statements.size();i+=2) {
 145                         int predicate = statements.get(i);
 146                         int object = statements.get(i+1);
 147                         ResourceInfo existing = infos.get(object);
 148                         if(existing != null) {
 149                 // Add all owners here for now and resolve the best owner later
 150                 existing.ownedResourcesWithPredicates.put(resource, predicate);
 151                             // Check if predicate is inverse, this just resolves all predicates to be inverse with ending "Inverse"..
 152                             String predicateUri = rewritePredicateURI(graph, predicate);
 153                             if (!predicateUri.endsWith("Inverse")) {
 154                                 existing.ownedBy.add(info);
 155                              if (LOGGER.isDebugEnabled()) {
 156                                     LOGGER.debug("    " + existing + " owns " + info + " with " + predicateUri);
 157                              }
 158                             }
 159                         }
 160                 }
 161         }
 162
 163     DataValueRepository repo = new DataValueRepository();
 164     DataValuePrinter printer = new DataValuePrinter(null, repo);
 165
 166     String printValue(Value value) throws Exception {
 167         StringBuilder sb = new StringBuilder();
 168         printer.setFormat(PrintFormat.SINGLE_LINE);
 169         printer.setOutput(sb);
 170
 171         Variant variant = value.value;
 172         printer.print(variant.getBinding(), variant.getValue());
 173         String formattedOutput = sb.toString();
 174         if (formattedOutput.length() > 100) {
 175             // Ok, value too long, lets calculate a hash for it and store first 100 chars as comment
 176               byte[] data = Bindings.getSerializerUnchecked(variant.getBinding()).serialize(variant.getValue());
 177               m.reset();
 178               m.update(data, 0, data.length);
 179               String hash = "\"" + new BigInteger(1, m.digest()).toString(16) + "\"";
 180               return hash + " // " + formattedOutput.substring(0, 100) + "..";
 181         } else {
 182             return formattedOutput;
 183         }
 184 //
 185 //        Variant variant = value.value;
 186 //        Datatype dt = variant.getBinding().type();
 187 //        if (Datatypes.STRING.equals(dt)) {
 188 //            String s = (String) variant.getValue(Bindings.STRING);
 189 //            if (s.contains("\n")) {
 190 //                return "\"\"\"" + s + "\"\"\"";
 191 //            } else {
 192 //                return "\"" + s + "\"";
 193 //            }
 194 //        } else if (Datatypes.BOOLEAN.equals(dt)) {
 195 //            Boolean i = (Boolean) variant.getValue(Bindings.BOOLEAN);
 196 //            return i ? "true" : "false";
 197 //        } else if (Datatypes.INTEGER.equals(dt)) {
 198 //            Integer i = (Integer) variant.getValue(Bindings.INTEGER);
 199 //            return i.toString();
 200 //        } else if (Datatypes.LONG.equals(dt)) {
 201 //            Long i = (Long) variant.getValue(Bindings.LONG);
 202 //            return i.toString();
 203 //        } else if (Datatypes.DOUBLE.equals(dt)) {
 204 //            Double d = (Double) variant.getValue();
 205 //            return d.toString();
 206 //        } else if (Datatypes.FLOAT.equals(dt)) {
 207 //            Float f = (Float) variant.getValue();
 208 //            return f.toString();
 209 //        } else if (Datatypes.STRING_ARRAY.equals(dt)) {
 210 //            return Arrays.toString((String []) variant.getValue());
 211 //        } else if (Datatypes.BOOLEAN_ARRAY.equals(dt)) {
 212 //            return Arrays.toString((boolean []) variant.getValue());
 213 //        } else if (Datatypes.INTEGER_ARRAY.equals(dt)) {
 214 //            return Arrays.toString((int []) variant.getValue());
 215 //        } else if (Datatypes.LONG_ARRAY.equals(dt)) {
 216 //            return Arrays.toString((long []) variant.getValue());
 217 //        } else if (Datatypes.DOUBLE_ARRAY.equals(dt)) {
 218 //            return Arrays.toString((double []) variant.getValue());
 219 //        } else if (Datatypes.FLOAT_ARRAY.equals(dt)) {
 220 //            return Arrays.toString((float []) variant.getValue());
 221 //        } else if (Datatypes.BYTE_ARRAY.equals(dt)) {
 222 //            return Arrays.toString((byte []) variant.getValue());
 223 ////        } else if (dt instanceof ArrayType) {
 224 ////            return Arrays.toString((Object []) variant.getValue());
 225 //        } else {
 226 //            byte[] data = Bindings.getSerializerUnchecked(variant.getBinding()).serialize(variant.getValue());
 227 //            m.reset();
 228 //            m.update(data, 0, data.length);
 229 //            return "\"" + new BigInteger(1, m.digest()).toString(16) + "\"";
 230 //        }
 231
 232     }
 233
 234         //      void fixInstanceOf(TransferableGraph1 graph, ResourceInfo info) {
 235         //              Identity id = getIdentity(graph, info.resource);
 236         //              if(id == null) return;
 237         //              if(id.definition instanceof Internal) {
 238         //                      Identity instanceOf = findExternal(graph, "http://www.simantics.org/Layer0-1.1/InstanceOf");
 239         //                      Identity library = findExternal(graph, "http://www.simantics.org/Layer0-1.1/Library");
 240         //                      info.statements.add(instanceOf.resource);
 241         //                      info.statements.add(library.resource);
 242         //              }
 243         //      }
 244
 245         public static String getExternalURI(TransferableGraph1 tg, External ext) {
 246                 String name = ext.name;
 247                 if(name.contains(" ")) name = name.replace(" ", "_").replaceAll("@", "_");//name = "\"" + name + "\"";
 248                 int parentId = ext.parent;
 249                 //if(parentId == 0) return ext.name;
 250                 //              else {
 251                 Identity id = TransferableGraphUtils.getIdentity(tg, parentId);
 252                 if(id.definition instanceof External) {
 253                         return getExternalURI(tg, (External)id.definition) + "/" + name;
 254                 } else if(id.definition instanceof Root) {
 255                         Root root = (Root)id.definition;
 256                         return "http:/" + root.name + "/" + name;
 257                 } else {
 258                         return null;
 259                 }
 260                 //              }
 261         }
 262
 263         public static String getExternalURI(TransferableGraph1 tg, int resource) {
 264                 Identity id = TransferableGraphUtils.getIdentity(tg, resource);
 265                 if(id == null) return null;
 266                 if(id.definition instanceof External) {
 267                         External ext = (External)id.definition;
 268                         return getExternalURI(tg, ext);
 269                 }
 270                 return null;
 271         }
 272
 273         String rewritePredicateURI(TransferableGraph1 graph, int predicate) {
 274
 275                 String uri = getExternalURI(graph, predicate);
 276                 if(uri == null) {
 277                         ResourceInfo info = infos.get(predicate);
 278                         if(info != null) return info.name;
 279                         return "_";
 280                 }
 281
 282                 for(String ontology : ontologies.keySet()) {
 283                         if(uri.contains(ontology)) {
 284                                 String key = ontologies.get(ontology);
 285                                 uri = uri.replace(ontology, key);
 286                                 referencedOntologies.add(ontology);
 287                         }
 288                 }
 289
 290                 uri = uri.replace("/", ".");
 291
 292                 return uri;
 293
 294         }
 295
 296         static void indent(StringBuilder output, int indent) {
 297                 for(int i=0;i<indent;i++)
 298                     output.append("  ");
 299         }
 300
 301         String printBlank(TransferableGraph1 graph, String predicateURI2, ResourceInfo info, int indent) {
 302
 303                 if(info.hasURI)
 304                     return null;
 305
 306                 StringBuilder output = new StringBuilder();
 307                 indent(output, indent);
 308                 output.append(predicateURI2 + " " + info.name + "\n");
 309
 310                 if (info.ownedResourcesWithPredicates.isEmpty()) {
 311                     String uri = printURI(graph, info, false, indent, false);
 312                     if (uri != null)
 313                         output.append(uri);
 314                 }
 315 //              if(info.owner < 0) {
 316 //                      printURI(graph, info, false, indent);
 317 //              }
 318                 return output.toString();
 319         }
 320
 321         static long longStm(int predicate, int object) {
 322                 return (predicate<<32) | (object & 0xffffffffL);
 323         }
 324
 325
 326     private void addInlineStatement(TransferableGraph1 graph, Map<String, Set<String>> statements, String predicate, ResourceInfo objectInfo, int indent) {
 327         Set<String> objects = statements.get(predicate);
 328         if(objects == null) {
 329             objects = new TreeSet<>();
 330             statements.put(predicate, objects);
 331         }
 332         String uri = printURI(graph, objectInfo, false, indent + 1, true);
 333         if (uri != null) {
 334             // TODO: this is not the right place to remove trailing newline
 335             uri = uri.endsWith("\n") ? uri.substring(0, uri.length() - 2) : uri;
 336             objects.add(uri);
 337         }
 338         objectInfo.inlined = true;
 339     }
 340
 341
 342         void addStatement(Map<String,Set<String>> statements, String predicate, String object) {
 343             // TODO: fix this
 344             if (predicate.endsWith("Inverse"))
 345                 return;
 346                 Set<String> objects = statements.get(predicate);
 347                 if(objects == null) {
 348                         objects = new TreeSet<>();
 349                         statements.put(predicate, objects);
 350                 }
 351                 objects.add(object);
 352         }
 353
 354         String printURI(TransferableGraph1 graph, ResourceInfo info, boolean requireURI, int indent, boolean inline) {
 355
 356                 if(requireURI && !info.hasURI)
 357                     return null;
 358
 359                 // Check if this ResourceInfo is already inlined with some other ResourceInfo
 360                 if (info.inlined)
 361                     return null;
 362
 363                 Map<String,Set<String>> statements = new TreeMap<>();
 364                 Identity consistsOf = TransferableGraphUtils.findExternal(graph, "http://www.simantics.org/Layer0-1.1/ConsistsOf");
 365                 TLongHashSet processed = new TLongHashSet();
 366                 for(int i=0;i<info.owned.size();i+=2) {
 367                         long stmId = longStm(info.owned.get(i), info.owned.get(i+1));
 368                         processed.add(stmId);
 369                 }
 370
 371                 TIntArrayList rawStatements = TransferableGraphUtils.getStatements(graph, info.resource);
 372                 for(int i=0;i<rawStatements.size();i+=2) {
 373                         long stmId = longStm(rawStatements.get(i), rawStatements.get(i+1));
 374                         if(!processed.add(stmId)) continue;
 375                         if(consistsOf.resource == rawStatements.get(i)) continue;
 376                         String predicateURI = rewritePredicateURI(graph, rawStatements.get(i));
 377                         ResourceInfo objectInfo = infos.get(rawStatements.get(i+1));
 378                         if(objectInfo == null) {
 379                                 String objectURI = rewritePredicateURI(graph, rawStatements.get(i+1));
 380                                 addStatement(statements, predicateURI, objectURI);
 381                         } else if (objectInfo.ownedBy.size() == 1 && objectInfo.ownedBy.contains(info)) {
 382                             // inline printing with _
 383                             addInlineStatement(graph, statements, predicateURI, objectInfo, indent);
 384                         } else {
 385                                 addStatement(statements, predicateURI, objectInfo.name);
 386                         }
 387                 }
 388
 389                 HashSet<ResourceInfo> debug = new HashSet<>();
 390                 info.ownedResourcesWithPredicates.forEachEntry(new TIntIntProcedure() {
 391
 392             @Override
 393             public boolean execute(int owner, int predicate) {
 394                 ResourceInfo ownerInfo = infos.get(owner);
 395                 debug.add(ownerInfo);
 396 //                ResourceInfo predicateInfo = infos.get(predicate);
 397 //                debug.add(predicateInfo);
 398                 return true;
 399             }
 400         });
 401
 402                 StringBuilder output = new StringBuilder();
 403
 404                 if(indent == 0 || inline) {
 405                         if("ROOT".equals(info.name)) {
 406                                 output.append("ROOT=<http:/>");
 407                         } else if (info.aliasURI != null) {
 408                                 output.append(info.name + " = <" + info.aliasURI + ">");
 409                         } else {
 410                             if (inline)
 411                                 System.out.println("asdasd");
 412                                 output.append(inline ? "_" : info.name);
 413                         }
 414                         Set<String> instanceOfs = statements.get("L0.InstanceOf");
 415                         if(instanceOfs != null) {
 416                                 for(String instanceOf : instanceOfs) {
 417                                         output.append(" : " + instanceOf);
 418                                 }
 419                         }
 420                         Set<String> subrelationOfs = statements.get("L0.SubrelationOf");
 421                         if(subrelationOfs != null) {
 422                                 for(String subrelationOf : subrelationOfs) {
 423                                         output.append(" <R " + subrelationOf);
 424                                 }
 425                         }
 426                         Set<String> inherits = statements.get("L0.Inherits");
 427                         if(inherits != null) {
 428                                 for(String inherit : inherits) {
 429                                         output.append(" <T " + inherit);
 430                                 }
 431                         }
 432                         output.append("\n");
 433                 }
 434
 435                 if(info.newResource)
 436                         output.append("  @L0.new\n");
 437
 438                 for(Map.Entry<String, Set<String>> entry : statements.entrySet()) {
 439                         String predicate = entry.getKey();
 440                         if("L0.InstanceOf".equals(predicate)) continue;
 441                         if("L0.SubrelationOf".equals(predicate)) continue;
 442                         if("L0.Inherits".equals(predicate)) continue;
 443                         if("L0.PartOf".equals(predicate)) continue;
 444                         Set<String> objects = entry.getValue();
 445                         indent(output, indent+1);
 446                         if(objects.size() == 1) {
 447                                 output.append(predicate + " " + objects.iterator().next() + "\n");
 448                         } else{
 449                                 output.append(predicate + "\n");
 450                                 for(String object : objects) {
 451                                         indent(output, indent+1);
 452                                         output.append("  " + object + "\n");
 453                                 }
 454                         }
 455                 }
 456
 457                 for(int i=0;i<info.owned.size();i+=2) {
 458                         String predicateURI = rewritePredicateURI(graph, info.owned.get(i));
 459                         ResourceInfo ownedInfo = infos.get(info.owned.get(i+1));
 460                         String blank = printBlank(graph, predicateURI, ownedInfo, indent+1);
 461                         if (blank != null)
 462                             output.append(blank);
 463                 }
 464
 465                 return output.toString();
 466         }
 467
 468     void prettyPrint(Path input, Path output) throws Exception {
 469
 470                 System.out.format("Converting exported shared ontology%n\t" + input.toString() + "%nto bundle-compatible ontology%n\t" + output.toString());
 471                 try (InputStream is = new BufferedInputStream(Files.newInputStream(input), 128*1024)) {
 472                         DataInput dis = new DataInputStream(is);
 473                         org.simantics.databoard.container.DataContainer container =
 474                                         DataContainers.readFile(dis);
 475                         Binding binding = TransferableGraph1.BINDING;
 476                         TransferableGraph1 graph = (TransferableGraph1)container.content.getValue(binding);
 477                         prettyPrint(graph);
 478                         Files.write(output, this.output.toString().getBytes());
 479
 480                 }
 481
 482         }
 483
 484         static Map<String,String> knownOntologies = new HashMap<>();
 485
 486         static {
 487                 knownOntologies.put("http://www.simantics.org/Layer0-1.1", "L0");
 488                 knownOntologies.put("http://www.simantics.org/Layer0X-1.1", "L0X");
 489                 knownOntologies.put("http://www.simantics.org/Modeling-1.2", "MOD");
 490                 knownOntologies.put("http://www.simantics.org/Diagram-2.2", "DIA");
 491                 knownOntologies.put("http://www.simantics.org/Structural-1.2", "STR");
 492                 knownOntologies.put("http://www.simantics.org/Document-1.2", "DOC");
 493                 knownOntologies.put("http://www.simantics.org/Documentation-1.2", "DOCU");
 494                 knownOntologies.put("http://www.simantics.org/G2D-1.1", "G2D");
 495                 knownOntologies.put("http://www.simantics.org/SelectionView-1.2", "SEL");
 496                 knownOntologies.put("http://www.simantics.org/Viewpoint-1.2", "VP");
 497                 knownOntologies.put("http://www.simantics.org/Image2-1.2", "IMAGE2");
 498                 knownOntologies.put("http://www.simantics.org/GraphFile-0.1", "GRAPHFILE");
 499                 knownOntologies.put("http://www.simantics.org/Project-1.2", "PROJECT");
 500                 knownOntologies.put("http://www.semantum.fi/Simupedia-1.0", "SIMUPEDIA");
 501                 knownOntologies.put("http://www.semantum.fi/SimupediaWorkbench-1.0", "SIMUPEDIA_WORKBENCH");
 502         }
 503
 504
 505         void prettyPrint(TransferableGraph1 graph) throws Exception {
 506
 507             if (LOGGER.isDebugEnabled())
 508                 LOGGER.debug("Starting prettyPrint for TransferableGraph with " + graph.resourceCount + " resources, " + graph.identities + " identities, " + graph.statements.length + " statements and " + graph.values.length + " values");
 509
 510                 for(Identity id : graph.identities) {
 511                         if(id.definition instanceof Internal) {
 512                                 Internal internal = (Internal)id.definition;
 513                                 Identity parent = TransferableGraphUtils.getIdentity(graph, internal.parent);
 514                                 if(parent.definition instanceof External) {
 515                         if (LOGGER.isDebugEnabled())
 516                             LOGGER.debug("Resolving internal identity " + id);
 517                                         String name = "BASE";
 518                                         ResourceInfo info = new ResourceInfo(true, name, id.resource, -1);
 519                                         info.aliasURI = TransferableGraphUtils.getURI(graph, id.resource);
 520                                         info.newResource = true;
 521                                         infos.put(id.resource, info);
 522                     if (LOGGER.isDebugEnabled())
 523                         LOGGER.debug("    which parent is external " + parent + " and has an aliasURI " + info.aliasURI) ;
 524                                         for(Identity child : TransferableGraphUtils.getChildren(graph, id)) {
 525                                                 recurseURI(graph, child, name, info.resource);
 526                                         }
 527                                         if (LOGGER.isDebugEnabled())
 528                                             LOGGER.debug("    and has " + (infos.size() - 1) + " children");
 529                                 }
 530                         } else if (id.definition instanceof External) {
 531                                 External ext = (External)id.definition;
 532                                 // Try to detect shared libraries
 533                                 if(ext.name.contains("@")) {
 534
 535                                     if (LOGGER.isDebugEnabled())
 536                                         LOGGER.debug("Detected an external shared library " + ext);
 537
 538                                         int index = ext.name.indexOf('@');
 539                                         String prefix = ext.name.substring(0, index);
 540                                         int index2 = ext.name.indexOf('/', index);
 541                                         String ontology = index2 == -1 ? ext.name : ext.name.substring(0, index2);
 542                                         String uri = TransferableGraphUtils.getURI(graph, id.resource);
 543
 544                                         if (LOGGER.isDebugEnabled())
 545                                             LOGGER.debug("    which was resolved as URI=" + uri + " and prefix " + prefix);
 546
 547                                         ontologies.put(uri, prefix);
 548
 549                                 } else if (ext.name.contains("-")) {
 550                                     if (LOGGER.isDebugEnabled())
 551                                         LOGGER.debug("Resolving possible ontology " + ext);
 552                                         String uri = TransferableGraphUtils.getURI(graph, id.resource);
 553                                 Matcher m = versionExtractPattern.matcher(uri);
 554                                 if (m.matches()) {
 555                                         if(!ontologies.containsKey(uri)) {
 556                                                         int index = ext.name.indexOf('-');
 557                             String prefix = ext.name.substring(0, index);
 558                             if (LOGGER.isDebugEnabled())
 559                                 LOGGER.debug("    and it was resolved as URI=" + uri + " and prefix " + prefix);
 560                             ontologies.put(uri, prefix);
 561                                         }
 562                                 }
 563                                 }
 564                         }
 565                 }
 566                 // Discover other resources
 567                 if (LOGGER.isDebugEnabled())
 568                     LOGGER.debug("Discovering other resources..");
 569
 570                 TIntArrayList todo = new TIntArrayList();
 571                 for(ResourceInfo info : infos.valueCollection())
 572                         todo.add(info.resource);
 573
 574                 while(!todo.isEmpty()) {
 575                         int resource = todo.removeAt(todo.size()-1);
 576                         discoverBlank(graph, resource, todo);
 577                 }
 578                 for(ResourceInfo info : infos.valueCollection())
 579                         discoverOwners(graph, info);
 580                 //                      for(ResourceInfo info : infos.valueCollection())
 581                 //                              fixInstanceOf(graph, info);
 582
 583         for (ResourceInfo info : infos.valueCollection()) {
 584 //          Old implementation
 585 //            if (info.owner >= 0) {
 586 //                ResourceInfo ownerInfo = infos.get(info.owner);
 587 //                System.out.println("originalOwner : " + info.owner + " originalPredicate: " + info.ownerPredicate);
 588 //                ownerInfo.owned.add(info.ownerPredicate);
 589 //                ownerInfo.owned.add(info.resource);
 590 //            }
 591
 592             if (!info.ownedResourcesWithPredicates.isEmpty() && info.ownedResourcesWithPredicates.size() == 1) {
 593                 info.ownedResourcesWithPredicates.forEachEntry(new TIntIntProcedure() {
 594
 595                     @Override
 596                     public boolean execute(int owner, int predicate) {
 597                         ResourceInfo ownerInfo = infos.get(owner);
 598                         ownerInfo.owned.add(predicate);
 599                         ownerInfo.owned.add(info.resource);
 600                         return false;
 601                     }
 602                 });
 603             }
 604         }
 605
 606         // Resolve inverses from ownedBy list
 607         for (ResourceInfo info : infos.valueCollection()) {
 608             for (int i = 0; i < info.owned.size(); i+=2) {
 609                 int object = info.owned.get(i+1);
 610                 ResourceInfo inf = infos.get(object);
 611                 if (inf != null) {
 612                     info.ownedBy.remove(inf);
 613                 }
 614             }
 615         }
 616
 617                 TreeMap<String,ResourceInfo> order = new TreeMap<>();
 618                 for(ResourceInfo info : infos.valueCollection())
 619                         order.put(info.name, info);
 620
 621                 for(ResourceInfo info : order.values()) {
 622                         String uri = printURI(graph, info, true, 0, false);
 623                         if (uri != null)
 624                             output.append(uri);
 625                 }
 626
 627                 for (ResourceInfo info : order.values()) {
 628                     if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) {
 629                         String uri = printURI(graph, info, false, 0, false);
 630                         if (uri != null)
 631                             output.append(uri);
 632                     }
 633                 }
 634 //              for(ResourceInfo info : order.values())
 635 //                      if(!info.hasURI && info.owner < 0)
 636 //                              printURI(graph, info, false, 0);
 637
 638                 StringBuilder refs = new StringBuilder();
 639                 for(String ontology : referencedOntologies) {
 640                         String key = ontologies.get(ontology);
 641                         refs.append(key + " = <" + ontology + ">\n");
 642                 }
 643                 if (!referencedOntologies.isEmpty())
 644                     refs.append("\n");
 645                 output.insert(0, refs.toString());
 646
 647         }
 648
 649     public static String print(TransferableGraph1 tg) throws Exception {
 650                 StringBuilder b = new StringBuilder();
 651                 new PrettyPrintTG(b).prettyPrint(tg);
 652                 return b.toString();
 653         }
 654
 655         public static void main(String[] args) throws Exception {
 656                 if (args.length < 1) {
 657                         System.out.println("Required arguments: <input .sharedOntology file> [<output .tg file>]");
 658                 } else if (args.length < 2) {
 659                         Path input = Paths.get(args[0]);
 660                         Path output = input.getParent().resolve(input.getName(input.getNameCount()-1) + ".fixed");
 661                         new PrettyPrintTG().prettyPrint(input, output);
 662                 } else {
 663                         new PrettyPrintTG().prettyPrint(Paths.get(args[0]), Paths.get(args[1]));
 664                 }
 665         }
 666
 667 }