Clean up and support internal seed resources in tg export 02/1402/2
authorAntti Villberg <antti.villberg@semantum.fi>
Mon, 29 Jan 2018 07:27:55 +0000 (09:27 +0200)
committerTuukka Lehtonen <tuukka.lehtonen@semantum.fi>
Mon, 29 Jan 2018 10:20:58 +0000 (12:20 +0200)
refs #7728

Change-Id: I95abd44fe4dea1ec639c4b8a328bdbfb0de3d4ae

16 files changed:
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/adapter/impl/DefaultPasteHandler.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/adapter/impl/SharedOntologyCopyHandler.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/ConsistsOfProcess.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/DomainProcessor3.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/DomainProcessorState.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/ModelTransferableGraphSource.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/ModelTransferableGraphSourceRequest.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/Subgraphs.java [deleted file]
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TGConfigurer.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TGConfigurer2.java [new file with mode: 0644]
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TGRepresentationUtils.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphConfiguration2.java
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest.java [deleted file]
bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest2.java [deleted file]
bundles/org.simantics.graph.db/src/org/simantics/graph/db/StreamingTransferableGraphImportProcess.java
bundles/org.simantics.modeling/src/org/simantics/modeling/adapters/CompositeCopyHandler.java

index 6b30e4ddb576c3424ba6283dacedf29af7a4f607..ccef12ebf07c3b18b016db876656f0ca3f1a1df8 100644 (file)
@@ -31,7 +31,8 @@ import org.simantics.db.layer0.util.RemoverUtil;
 import org.simantics.db.layer0.util.SimanticsClipboard;
 import org.simantics.db.layer0.util.SimanticsClipboard.Representation;
 import org.simantics.db.layer0.util.SimanticsKeys;
-import org.simantics.db.layer0.util.TransferableGraphConfiguration2.RootSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.graph.db.IImportAdvisor;
 import org.simantics.graph.db.IImportAdvisor2;
 import org.simantics.graph.db.IImportAdvisor2.RootInfo;
@@ -119,8 +120,8 @@ public class DefaultPasteHandler extends PasteHandlerAdapter {
                
                ModelTransferableGraphSource mtgs = (ModelTransferableGraphSource)tgs;
                
-               loop: for(RootSpec spec : mtgs.getConfiguration().roots) {
-                       if(!spec.internal) continue;
+               loop: for(SeedSpec spec : mtgs.getConfiguration().seeds) {
+                       if(SeedSpecType.SPECIAL_ROOT.equals(spec.specType)) continue;
                        for(RootInfo info : roots) {
                                if(spec.name.equals(info.root.name)) {
                                        result.add(info.resource);
index 16ec6e7cbaac927092d40c3e7ffa33efb3fbbc6f..3c7dfb40a4e5d5f21024683b31c518f5f4065880 100644 (file)
@@ -19,7 +19,8 @@ import org.simantics.db.Resource;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.util.TGConfigurer;
 import org.simantics.db.layer0.util.TransferableGraphConfiguration2;
-import org.simantics.db.layer0.util.TransferableGraphConfiguration2.RootSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 
 public class SharedOntologyCopyHandler extends DefaultCopyHandler {
 
@@ -38,7 +39,7 @@ public class SharedOntologyCopyHandler extends DefaultCopyHandler {
 
        Resource root = resources.iterator().next();
        String uri = graph.getURI(root);
-       Collection<RootSpec> roots = Collections.singletonList(new RootSpec(root, uri, true));
+       Collection<SeedSpec> roots = Collections.singletonList(new SeedSpec(root, uri, SeedSpecType.ROOT));
        return new TGConfigurer(graph, true, false).roots(roots).create();
        
     }
index a2e64868f7c21d43c1456c4662810c20f6ca4ed6..4124add429dd76d4ae2756a6b3e0404e0d214f01 100644 (file)
@@ -14,6 +14,8 @@ import org.simantics.db.common.request.ReadRequest;
 import org.simantics.db.common.utils.Logger;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.db.procedure.AsyncContextMultiProcedure;
 import org.simantics.db.procedure.Procedure;
 import org.simantics.db.service.DirectQuerySupport;
@@ -22,39 +24,53 @@ import org.simantics.utils.datastructures.Pair;
 
 class ConsistsOfProcess {
 
-       final List<InternalEntry> result;
+       final List<ConsistsOfProcessEntry> result;
        final Set<Resource> childrenWithNoName;
-       final AsyncContextMultiProcedure<InternalEntry, Resource> structure;
-       final AsyncContextMultiProcedure<InternalEntry, Resource> names;
+       final AsyncContextMultiProcedure<ConsistsOfProcessEntry, Resource> structure;
+       final AsyncContextMultiProcedure<ConsistsOfProcessEntry, Resource> names;
 
-       public static Pair<List<InternalEntry>,Set<Resource>> walk(ReadGraph graph, ResourceMap<ExtentStatus> status, Collection<Resource> resources, Set<Resource> exclusions, boolean ignoreVirtual) throws DatabaseException {
-       ConsistsOfProcess process = new ConsistsOfProcess(graph, status, resources, exclusions, ignoreVirtual);
+       public static Pair<List<ConsistsOfProcessEntry>,Set<Resource>> walk(ReadGraph graph, Collection<SeedSpec> specs, boolean ignoreVirtual) throws DatabaseException {
+               return walk(graph, null, specs, ignoreVirtual);
+       }
+
+       public static Pair<List<ConsistsOfProcessEntry>,Set<Resource>> walk(ReadGraph graph, ResourceMap<ExtentStatus> status, Collection<SeedSpec> specs, boolean ignoreVirtual) throws DatabaseException {
+               
+               Collection<ConsistsOfProcessEntry> entries = new ArrayList<>();
+               for(SeedSpec r : specs) {
+                       if(SeedSpecType.INTERNAL.equals(r.specType))
+                           entries.add(new ConsistsOfProcessEntry(null, r.resource, true));
+                       else
+                               entries.add(new ConsistsOfProcessEntry(null, r.resource, false));
+               }
+       ConsistsOfProcess process = new ConsistsOfProcess(graph, status, entries, ignoreVirtual);
        return Pair.make(process.result, process.childrenWithNoName);
+       
     }
     
-    static class InternalEntry {
-       public InternalEntry parent;
+    static class ConsistsOfProcessEntry {
+       public ConsistsOfProcessEntry parent;
        public Resource resource;
-       public String name;
+       public boolean internal;
        public boolean valid = true;
-       InternalEntry(InternalEntry parent, Resource resource, String name) {
+       public String name = null;
+       ConsistsOfProcessEntry(ConsistsOfProcessEntry parent, Resource resource, boolean internal) {
                this.parent = parent;
                this.resource = resource;
-               this.name = name;
+               this.internal = internal;
        }
     }
        
-    private ConsistsOfProcess(ReadGraph graph, ResourceMap<ExtentStatus> status, final Collection<Resource> resources, final Set<Resource> exclusions, final boolean ignoreVirtual) throws DatabaseException {
+    private ConsistsOfProcess(ReadGraph graph, ResourceMap<ExtentStatus> status, final Collection<ConsistsOfProcessEntry> entries, final boolean ignoreVirtual) throws DatabaseException {
 
                final Layer0 L0 = Layer0.getInstance(graph);
                final DirectQuerySupport dqs = graph.getService(DirectQuerySupport.class);
                
-               result = new ArrayList<InternalEntry>();
+               result = new ArrayList<>();
                childrenWithNoName = new HashSet<>();
-               names = dqs.compileForEachObject(graph, L0.HasName, new AsyncContextMultiProcedure<InternalEntry, Resource>() {
+               names = dqs.compileForEachObject(graph, L0.HasName, new AsyncContextMultiProcedure<ConsistsOfProcessEntry, Resource>() {
 
                        @Override
-                       public void execute(AsyncReadGraph graph, InternalEntry entry, Resource nameResource) {
+                       public void execute(AsyncReadGraph graph, ConsistsOfProcessEntry entry, Resource nameResource) {
                
                                if(status != null)
                                        status.put(nameResource, ExtentStatus.EXCLUDED);
@@ -88,7 +104,7 @@ class ConsistsOfProcess {
                        }
 
                        @Override
-                       public void finished(AsyncReadGraph graph, InternalEntry entry) {
+                       public void finished(AsyncReadGraph graph, ConsistsOfProcessEntry entry) {
                            if(entry.valid) {
                                if(entry.name != null) {
                                    result.add(entry);
@@ -103,15 +119,16 @@ class ConsistsOfProcess {
                        }
                });
                
-               structure = dqs.compileForEachObject(graph, L0.ConsistsOf, new AsyncContextMultiProcedure<InternalEntry, Resource>() {
+               structure = dqs.compileForEachObject(graph, L0.ConsistsOf, new AsyncContextMultiProcedure<ConsistsOfProcessEntry, Resource>() {
 
                        @Override
-                       public void execute(AsyncReadGraph graph, InternalEntry parent, Resource child) {
-                               
-                               if(exclusions.contains(child)) return;
+                       public void execute(AsyncReadGraph graph, ConsistsOfProcessEntry parent, Resource child) {
+
+                               if(status != null)
+                                       if(ExtentStatus.EXCLUDED.equals(status.get(child))) return;
                                
                                if(!ignoreVirtual || child.isPersistent()) {
-                                       InternalEntry entry = new InternalEntry(parent, child, null);
+                                       ConsistsOfProcessEntry entry = new ConsistsOfProcessEntry(parent, child, false);
                                        dqs.forEachObjectCompiled(graph, child, entry, structure);
                                        dqs.forEachObjectCompiled(graph, child, entry, names);
                                }
@@ -119,7 +136,7 @@ class ConsistsOfProcess {
                        }
 
                        @Override
-                       public void finished(AsyncReadGraph graph, InternalEntry parent) {
+                       public void finished(AsyncReadGraph graph, ConsistsOfProcessEntry parent) {
                        }
 
                        @Override
@@ -133,9 +150,12 @@ class ConsistsOfProcess {
 
                        @Override
                        public void run(ReadGraph graph) throws DatabaseException {
-                               for(Resource r  : resources) {
-                                       InternalEntry root = new InternalEntry(null, r, null);
-                                       dqs.forEachObjectCompiled(graph, r, root, structure);
+                               for(ConsistsOfProcessEntry entry  : entries) {
+                                       dqs.forEachObjectCompiled(graph, entry.resource, entry, structure);
+                                       if(entry.internal) {
+                                               // For roots names are not processed
+                                               dqs.forEachObjectCompiled(graph, entry.resource, entry, names);
+                                       }
                                }
                        }
                        
index 20856d4ced9de92d68b013cb6c545bfc95bdfdff..c7bc380e5435cbe5e359185448d006de8eda7a45 100644 (file)
@@ -28,7 +28,7 @@ import org.simantics.db.common.utils.NameUtils;
 import org.simantics.db.exception.CancelTransactionException;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.layer0.util.ConsistsOfProcess.InternalEntry;
+import org.simantics.db.layer0.util.ConsistsOfProcess.ConsistsOfProcessEntry;
 import org.simantics.db.layer0.util.ModelTransferableGraphSourceRequest.Expansion3;
 import org.simantics.db.service.CollectionSupport;
 import org.simantics.db.service.SerialisationSupport;
@@ -57,7 +57,6 @@ public class DomainProcessor3 {
     int id = 0;
 
     Set<Resource> fringe = null;
-    Set<Resource> exclusions = null;
     Function1<Statement,ExclusionDecision> exclusionFunction = null;
     Set<Resource> predicates = null;
     Map<Resource,Boolean> isRelatedToPredicates = null;
@@ -108,7 +107,6 @@ public class DomainProcessor3 {
         ids = state.ids;
         status = cs.createMap(ExtentStatus.class);
         predicates = cs.createSet();
-        exclusions = cs.createSet();
         exclusionFunction = conf.exclusionFunction;
         fringe = new TreeSet<Resource>();
         isRelatedToPredicates = cs.createMap(Boolean.class);
@@ -117,17 +115,10 @@ public class DomainProcessor3 {
 
         for(Map.Entry<Resource, ExtentStatus> entry : conf.preStatus.entrySet()) {
             status.put(entry.getKey(), entry.getValue());
-            if(ExtentStatus.EXCLUDED.equals(entry.getValue())) exclusions.add(entry.getKey());
-            if(ExtentStatus.INTERNAL.equals(entry.getValue())) fringe.add(entry.getKey());
         }
 
        if(PROFILE)
                startupTime += System.nanoTime();
-       
-//        for(RootSpec p : conf.roots) {
-//             if(p.internal)
-//                     fringe.add(p.resource);
-//        }
 
     }
     
@@ -185,10 +176,10 @@ public class DomainProcessor3 {
                
                 if(graph.isSubrelationOf(predicate, L0.IsRelatedTo)) {
                        isRelatedTo = Boolean.TRUE;
-                    if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("isRelatedToPredicates4 => " + NameUtils.getSafeName(graph, predicate));
+                    if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("isRelatedToPredicates4 => " + NameUtils.getSafeName(graph, predicate));
                 } else {
                     if (!graph.hasStatement(predicate)) {
-                        if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("FOUND DEAD PREDICATE (no statements): " + predicate);
+                        if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("FOUND DEAD PREDICATE (no statements): " + predicate);
                         deadPredicates.add(predicate);
                         // Prevents ModelTransferableGraphSource from
                         // trying to export these statements.
@@ -219,14 +210,13 @@ public class DomainProcessor3 {
                 Resource predicate = stm.getPredicate();
                 Resource object = stm.getObject();
 
-                if (exclusions.contains(object) || exclusions.contains(predicate))
-                    continue;
+                if(ExtentStatus.EXCLUDED.equals(status.get(predicate))) continue;
+                if(ExtentStatus.EXCLUDED.equals(status.get(object))) continue;
                 
                 if (exclusionFunction != null) {
                        ExclusionDecision decision = exclusionFunction.apply(stm);
                        if(ExclusionDecision.EXCLUDE_OBJECT.equals(decision)) {
                                status.put(object, ExtentStatus.EXCLUDED);
-                               exclusions.add(object);
                                continue;
                        }
                 }
@@ -239,10 +229,10 @@ public class DomainProcessor3 {
                         if(predicates.add(inverse)) schedule.add(inverse);
                         state.inverses.put(support.getTransientId(predicate), support.getTransientId(inverse));
                         state.inverses.put(support.getTransientId(inverse), support.getTransientId(predicate));
-                        if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("INVERSE FOR " + graph.getPossibleURI(predicate) + " => " + graph.getPossibleURI(inverse));
+                        if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("INVERSE FOR " + graph.getPossibleURI(predicate) + " => " + graph.getPossibleURI(inverse));
                     } else {
                         state.inverses.put(support.getTransientId(predicate), 0);
-                        if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("NO INVERSE FOR " + graph.getPossibleURI(predicate));
+                        if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("NO INVERSE FOR " + graph.getPossibleURI(predicate));
                     }
 
                 }
@@ -277,7 +267,7 @@ public class DomainProcessor3 {
     public void processValue(ReadGraph graph, Resource subject, int sId, final DomainProcessorState state) throws DatabaseException, IOException {
         final InputStream valueStream = tgs.getValueStream(graph, subject);
         if (valueStream != null) {
-            if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("[VALUE] " + NameUtils.getSafeName(graph, subject, true));
+            if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("[VALUE] " + NameUtils.getSafeName(graph, subject, true));
             state.valueOutput.writeInt(sId);
 
             if (conf.values) {
@@ -343,12 +333,12 @@ public class DomainProcessor3 {
         Boolean isRelatedTo = isRelatedToPredicates.get(predicate);
         if ((objectStatus !=  ExtentStatus.EXCLUDED) && isRelatedTo) {
 
-            if(ModelTransferableGraphSourceRequest.LOG) logStatementWithExtent(graph, "related", objectStatus, subject, predicate, object);
+            if(ModelTransferableGraphSourceRequest.DEBUG) logStatementWithExtent(graph, "related", objectStatus, subject, predicate, object);
 
             addToStream(predicate, object);
 
             if(objectStatus == null || objectStatus == ExtentStatus.PENDING) {
-                if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("[ADDED TO FRINGE] " + NameUtils.getSafeName(graph, object));
+                if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("[ADDED TO FRINGE] " + NameUtils.getSafeName(graph, object));
                 fringe.add(object);
             }
 
@@ -356,14 +346,14 @@ public class DomainProcessor3 {
 
             // Dead predicate
             if (deadPredicates.contains(predicate)) {
-                if(ModelTransferableGraphSourceRequest.LOG) logStatementWithExtent(graph, "excluding statement with dead predicate ", objectStatus, subject, predicate, object);
+                if(ModelTransferableGraphSourceRequest.DEBUG) logStatementWithExtent(graph, "excluding statement with dead predicate ", objectStatus, subject, predicate, object);
                 return;
             }
 
             // Weak predicate
             if(objectStatus == ExtentStatus.EXCLUDED) {
 
-                if(ModelTransferableGraphSourceRequest.LOG) logStatementWithExtent(graph, "weak reference to excluded object ", objectStatus, subject, predicate, object);
+                if(ModelTransferableGraphSourceRequest.DEBUG) logStatementWithExtent(graph, "weak reference to excluded object ", objectStatus, subject, predicate, object);
 
             } else {
 
@@ -377,11 +367,11 @@ public class DomainProcessor3 {
                         status.put(object, ExtentStatus.PENDING);
                     }
 
-                    if(ModelTransferableGraphSourceRequest.LOG) logStatementWithExtent(graph, "fully weak internal", objectStatus, subject, predicate, object);
+                    if(ModelTransferableGraphSourceRequest.DEBUG) logStatementWithExtent(graph, "fully weak internal", objectStatus, subject, predicate, object);
 
                 } else {
 
-                    if(ModelTransferableGraphSourceRequest.LOG) logStatementWithExtent(graph, "strong inverse internal ", objectStatus, subject, predicate, object);
+                    if(ModelTransferableGraphSourceRequest.DEBUG) logStatementWithExtent(graph, "strong inverse internal ", objectStatus, subject, predicate, object);
 
                 }
 
@@ -428,7 +418,7 @@ public class DomainProcessor3 {
         }
 
         status.put(subject, ExtentStatus.INTERNAL);
-        if(ModelTransferableGraphSourceRequest.LOG) ModelTransferableGraphSourceRequest.log("[INTERNAL] " + NameUtils.getSafeName(graph, subject, true));
+        if(ModelTransferableGraphSourceRequest.DEBUG) ModelTransferableGraphSourceRequest.log("[INTERNAL] " + NameUtils.getSafeName(graph, subject, true));
 
         int sId = support.getTransientId(subject);
 
@@ -476,12 +466,12 @@ public class DomainProcessor3 {
             }
 
             ExtentStatus subjectStatus = status.get(subject);
-            if(ModelTransferableGraphSourceRequest.LOG && subjectStatus != null) ModelTransferableGraphSourceRequest.log("EXISTING STATUS FOR " + graph.getPossibleURI(subject) + " - " + subjectStatus);
+            if(ModelTransferableGraphSourceRequest.DEBUG && subjectStatus != null) ModelTransferableGraphSourceRequest.log("EXISTING STATUS FOR " + graph.getPossibleURI(subject) + " - " + subjectStatus);
             if(subjectStatus == ExtentStatus.EXTERNAL || subjectStatus == ExtentStatus.EXCLUDED) continue;
             if(partOf && (subjectStatus == null || ExtentStatus.PENDING == subjectStatus) && graph.getPossibleURI(subject) != null) {
 
                 status.put(subject, ExtentStatus.EXTERNAL);
-                if(ModelTransferableGraphSourceRequest.LOG) {
+                if(ModelTransferableGraphSourceRequest.DEBUG) {
                     String uri = graph.getPossibleURI(subject);
                     if(uri == null) ModelTransferableGraphSourceRequest.log("[EXTERNAL]: No URI for " + subject);
                     else ModelTransferableGraphSourceRequest.log("[EXTERNAL] " + uri);
@@ -508,13 +498,13 @@ public class DomainProcessor3 {
             this.datatypeBinding = Bindings.getBindingUnchecked(Datatype.class);
             this.datatypeSerializer = graph.getService(Databoard.class).getSerializerUnchecked(this.datatypeBinding);
 
-            Pair<List<InternalEntry>,Set<Resource>> pair = ConsistsOfProcess.walk(graph, status, fringe, exclusions, ignoreVirtual); 
+            Pair<List<ConsistsOfProcessEntry>,Set<Resource>> pair = ConsistsOfProcess.walk(graph, status, conf.seeds, ignoreVirtual); 
             state.internalEntries = pair.first;
             
-            for(InternalEntry entry : state.internalEntries) {
+            for(ConsistsOfProcessEntry entry : state.internalEntries) {
                Resource r = entry.resource;
                 if (status.put(r, ExtentStatus.INTERNAL) == null) {
-                    if(ModelTransferableGraphSourceRequest.LOG) {
+                    if(ModelTransferableGraphSourceRequest.DEBUG) {
                         String URI = graph.getPossibleURI(r);
                         if(URI != null) ModelTransferableGraphSourceRequest.log("URI INTERNAL " + URI);
                         else ModelTransferableGraphSourceRequest.log("URI has no URI for " + r);
@@ -555,7 +545,7 @@ public class DomainProcessor3 {
     }
 
     void logStatementWithExtent(ReadGraph graph, String header, ExtentStatus status, int sId, int pId, int oId) throws DatabaseException {
-        if(ModelTransferableGraphSourceRequest.LOG) {
+        if(ModelTransferableGraphSourceRequest.DEBUG) {
             SerialisationSupport support = graph.getService(SerialisationSupport.class);
             String s = NameUtils.getURIOrSafeNameInternal(graph, support.getResource(sId));
             String p = NameUtils.getURIOrSafeNameInternal(graph, support.getResource(pId));
@@ -565,7 +555,7 @@ public class DomainProcessor3 {
     }
 
     void logStatementWithExtent(ReadGraph graph, String header, ExtentStatus status, Resource sId, Resource pId, Resource oId) throws DatabaseException {
-        if(ModelTransferableGraphSourceRequest.LOG) {
+        if(ModelTransferableGraphSourceRequest.DEBUG) {
             String s = NameUtils.getURIOrSafeNameInternal(graph, sId);
             String p = NameUtils.getURIOrSafeNameInternal(graph, pId);
             String o = NameUtils.getURIOrSafeNameInternal(graph, oId);
index 3f25410187768519082691dad43bd558f1c3d98b..e8d97255b7c1ba4cf68f77e899a3dbe571b86ec1 100644 (file)
@@ -32,6 +32,6 @@ public class DomainProcessorState {
 
        public SubMonitor monitor;
        public TGValueModifier valueModifier;
-       public List<ConsistsOfProcess.InternalEntry> internalEntries;
+       public List<ConsistsOfProcess.ConsistsOfProcessEntry> internalEntries;
 
 }
\ No newline at end of file
index 1d3cf61f54c6c6ad296b06a959f62dac66601537..95923c79946206805ef467211e5523c313c766ee 100644 (file)
@@ -27,8 +27,9 @@ import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.exception.RuntimeDatabaseException;
 import org.simantics.db.exception.ValidationException;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.layer0.util.ConsistsOfProcess.InternalEntry;
-import org.simantics.db.layer0.util.TransferableGraphConfiguration2.RootSpec;
+import org.simantics.db.layer0.util.ConsistsOfProcess.ConsistsOfProcessEntry;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.db.service.SerialisationSupport;
 import org.simantics.graph.db.TransferableGraphSource;
 import org.simantics.graph.representation.External;
@@ -68,34 +69,34 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                SerialisationSupport ss = graph.getService(SerialisationSupport.class);
 
                // At this point ids contains all internal resources. Now add roots and externals.
-               
+
                // Root Library
                state.ids.put(ss.getTransientId(graph.getRootLibrary()), state.id++);
-               
+
                // External roots - internal roots were already processed as internal resources by domain processor
-               for(RootSpec rs : configuration.roots) {
-                       if(!rs.internal) {
-                               int resourceId = ss.getTransientId(rs.resource);
+               for(SeedSpec spec : configuration.seeds) {
+                       if(SeedSpecType.SPECIAL_ROOT.equals(spec.specType)) {
+                               int resourceId = ss.getTransientId(spec.resource);
                                state.ids.put(resourceId, state.id++);
                                // The fixed roots have been seen as externals by domain processor. Now remove them from external set.
                                state.externals.remove(resourceId);
                        }
                }
-               
+
                this.externalBase = state.id;
 
                final Collection<String> errors = new HashSet<>();
 
                // All resource considered as not internal by domain processor. Can also contain roots.
                int[] externals = state.externals.toArray();
-               
+
                // Build up the state.externals, externalNames and externalParents
                for(int i=0;i<externals.length;i++) {
                        getId(graph, externals[i], errors);
                }
-               
+
                state.inverses.forEachEntry(new TIntIntProcedure() {
-                       
+
                        @Override
                        public boolean execute(int predicate, int inverse) {
                                try {
@@ -106,9 +107,9 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                                }
                                return true;
                        }
-                       
+
                });
-               
+
                if(!errors.isEmpty()) {
                        ArrayList<String> sorted = new ArrayList<>(errors);
                        Collections.sort(sorted);
@@ -120,15 +121,15 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                        }
                        throw new DatabaseException(message.toString());
                }
-               
+
                this.resourceCount = state.id;
-               
+
                state.extensions.put(ExternalDownloadBean.EXTENSION_KEY, new Variant(ExternalDownloadBean.BINDING, new ExternalDownloadBean(downloads)));
-               
+
        }
 
        int indent = 0;
-       
+
        public boolean validateExternal(Resource ext) {
                if(configuration.validate) {
                        ExtentStatus status = configuration.preStatus.get(ext);
@@ -139,14 +140,14 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                }
                return true;
        }
-       
+
        private Resource getResource(ReadGraph graph, int r) throws DatabaseException {
                SerialisationSupport ss = graph.getService(SerialisationSupport.class);
                return ss.getResource(r);
        }
-       
+
        final public int getExistingId(ReadGraph graph, int r) throws DatabaseException {
-               
+
                int ret = state.ids.get(r);
                if(ret != -1) {
                        return ret;
@@ -156,7 +157,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                }
 
        }
-       
+
        /*
         * 
         * @return -2 if r is not really external and the statement should be excluded
@@ -166,10 +167,10 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
 
 //             // First external is root library
 //             if(r == rootId) return internalCount;
-               
+
                SerialisationSupport ss = graph.getService(SerialisationSupport.class);
                Layer0 L0 = Layer0.getInstance(graph);
-               
+
                if(state.ids.containsKey(r)) {
                    int ret = state.ids.get(r);
                    if(ret == -1) {
@@ -185,7 +186,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                errors.add("Illegal reference to " + graph.getPossibleURI(getResource(graph, r)));
                return -2;
             }
-                       Collection<Resource> parents = graph.getObjects(res, L0.PartOf);                        
+                       Collection<Resource> parents = graph.getObjects(res, L0.PartOf);
                        if(parents.size() != 1) {
                                throw new ValidationException("Reference to external resource " 
                                                + NameUtils.getSafeName(graph, getResource(graph, r), true) + " without unique uri (" + parents.size() + " parents).");
@@ -215,27 +216,36 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                        return state.id++;
                }
        }
-       
+
        @Override
        public DataContainer getHeader() throws Exception {
            return null;
        }
-       
+
        @Override
        public int getResourceCount() {
                return resourceCount;
        }
-       
+
+       private int countRootSeeds() {
+               int result = 0;
+               for(SeedSpec spec : configuration.seeds) {
+                       if(SeedSpecType.INTERNAL.equals(spec.specType)) continue;
+                       result++;
+               }
+               return result;
+       }
+
        @Override
        public int getIdentityCount() {
-               return configuration.roots.size() + state.externals.size() + state.internalEntries.size() + 1;
+               return countRootSeeds() + state.externals.size() + state.internalEntries.size() + 1;
        }
-       
+
        @Override
        public int getStatementCount() {
                return state.statementCount;
        }
-       
+
        @Override
        public int getValueCount() {
                return state.valueCount;
@@ -243,18 +253,18 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
 
        @Override
        public void forStatements(ReadGraph graph, TransferableGraphSourceProcedure<int[]> procedure) throws Exception {
-               
+
                int[] value = new int[4];
                long length = state.otherStatementsInput.length();
                state.otherStatementsInput.position(0);
-               
+
                while(state.otherStatementsInput.position() < length && !state.monitor.isCanceled()) {
-                       
+
                        int s = state.otherStatementsInput.readInt();
                        int subjectId = state.ids.get(s);
-                       
+
                        boolean exclude = subjectId == -1;
-                       
+
                        int size = state.otherStatementsInput.readInt();
                        for(int i=0;i<size;i++) {
                                int p = state.otherStatementsInput.readInt();
@@ -265,7 +275,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                                        } else if(state.excludedShared.contains(o)) {
                                                System.err.println("excluding shared " + s + " " + p + " " + o);
                                        } else {
-                                               
+
                                                int objectId = getExistingId(graph, o);
                                                // The statement can be denied still
                                                if(objectId != -2) {
@@ -280,11 +290,11 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                                                        value[3] = objectId;
 
                                                        procedure.execute(value);
-                                                       
+
                                                } else {
                                                        System.err.println("Denied (" + NameUtils.getSafeName(graph, getResource(graph, s)) + ", " + NameUtils.getSafeName(graph, getResource(graph, p)) + "," + NameUtils.getSafeName(graph, getResource(graph, o)) + ")");
-                                               }                                               
-                                               
+                                               }
+
                                        }
                                } else {
                                        System.err.println("excluding shared " + s);
@@ -385,7 +395,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
 
        @Override
        public void forIdentities(ReadGraph graph, TransferableGraphSourceProcedure<Identity> procedure) throws Exception {
-               
+
                SerialisationSupport support = graph.getService(SerialisationSupport.class);
                Layer0 L0 = Layer0.getInstance(graph);
 
@@ -395,7 +405,8 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                TIntObjectMap<Identity> internalMap = new TIntObjectHashMap<>(100, 0.5f, Integer.MIN_VALUE);
 
                // Declare internal and external roots
-               for(RootSpec r : configuration.roots) {
+               for(SeedSpec r : configuration.seeds) {
+                       if(SeedSpecType.INTERNAL.equals(r.specType)) continue;
                        String typeId = r.type;
                        if (typeId == null) {
                                Resource type = graph.getPossibleType(r.resource, L0.Entity);
@@ -413,32 +424,44 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                        String name = externalNames.get(i);
                        procedure.execute(new Identity(externalBase + i, new External(parent,name)));
        }
-               
+
                if(state.internalEntries != null) {
-                       for(InternalEntry ie : state.internalEntries) {
-                           if(ie.parent != null) {
-                               if(ie.name != null) {
-                                   procedure.execute(resolveInternal(graph, support, ie, internalMap));
-                           } else {
-                               // In this case there is a child that has no HasName => this should be treated as a blank
-                               }
+                       for(ConsistsOfProcessEntry ie : state.internalEntries) {
+                               if(ie.parent != null) {
+                                       if(ie.name != null) {
+                                               procedure.execute(resolveInternal(graph, support, ie, internalMap));
+                                       } else {
+                                               // In this case there is a child that has no HasName => this should be treated as a blank
+                                       }
                                } else {
-                                       throw new DatabaseException("Invalid internal entry " + ie);
+                                       procedure.execute(resolveInternal(graph, support, ie, internalMap));
                                }
                        }
                }
-       
+
        }
-       
-       private Identity resolveInternal(ReadGraph graph, SerialisationSupport ss, InternalEntry entry, TIntObjectMap<Identity> internalMap) throws DatabaseException {
+
+       private Identity resolveInternal(ReadGraph graph, SerialisationSupport ss, ConsistsOfProcessEntry entry, TIntObjectMap<Identity> internalMap) throws DatabaseException {
                int id = state.ids.get(ss.getTransientId(entry.resource));
                Identity existing = internalMap.get(id);
                if(existing != null) return existing;
-               Identity parent = resolveInternal(graph, ss, entry.parent, internalMap);
-               Identity result = new Identity(id,
-                               new Internal(parent.resource, entry.name));
-               internalMap.put(id, result);
-               return result;
+
+               if(entry.parent == null) {
+                       Layer0 L0 = Layer0.getInstance(graph);
+                       Resource possibleParent = graph.getPossibleObject(entry.resource, L0.PartOf);
+                       if(possibleParent == null) throw new DatabaseException("Invalid root or internal parent path: " + entry.resource);
+                       int externalId = state.ids.get(ss.getTransientId(possibleParent));
+                       Identity result = new Identity(id,
+                                       new Internal(externalId, entry.name));
+                       internalMap.put(id, result);
+                       return result;
+               } else {
+                       Identity parent = resolveInternal(graph, ss, entry.parent, internalMap);
+                       Identity result = new Identity(id,
+                                       new Internal(parent.resource, entry.name));
+                       internalMap.put(id, result);
+                       return result;
+               }
        }
 
        @Override
@@ -467,7 +490,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
        public void reset() throws Exception {
            throw new UnsupportedOperationException();
        }
-       
+
        public long[] getResourceArray(ReadGraph graph) throws DatabaseException {
                final SerialisationSupport ss = graph.getService(SerialisationSupport.class);
                final long[] result = new long[state.ids.size()];
@@ -475,38 +498,38 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
 
                        @Override
                        public boolean execute(int a, int b) {
-                               
+
                                try {
                                        Resource r = ss.getResource(a);
                                        result[b] = r.getResourceId();
                                } catch (DatabaseException e) {
                                        e.printStackTrace();
                                }
-                               
+
                                return true;
-                               
+
                        }
                });
                return result;
        }
-       
+
        public DomainProcessorState getState() {
                return state;
        }
-       
+
        public void forResourceStatements(ReadGraph graph, TransferableGraphSourceProcedure<int[]> procedure) throws Exception {
-               
+
                int[] value = new int[4];
                long length = state.otherStatementsInput.length();
                state.otherStatementsInput.position(0);
-               
+
                while(state.otherStatementsInput.position() < length) {
-                       
+
                        int s = state.otherStatementsInput.readInt();
                        int subjectId = state.ids.get(s);
-                       
+
                        boolean exclude = subjectId == -1;
-                       
+
                        int size = state.otherStatementsInput.readInt();
                        for(int i=0;i<size;i++) {
                                int p = state.otherStatementsInput.readInt();
@@ -515,7 +538,7 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                                        if(state.excludedShared.contains(o)) {
                                                System.err.println("excluding shared " + s + " " + p + " " + o);
                                        } else {
-                                               
+
                                                int objectId = getExistingId(graph, o);
                                                // The statement can be denied still
                                                if(objectId != -2) {
@@ -530,11 +553,11 @@ public class ModelTransferableGraphSource implements TransferableGraphSource {
                                                        value[3] = o;
 
                                                        procedure.execute(value);
-                                                       
+
                                                } else {
                                                        System.err.println("Denied (" + NameUtils.getSafeName(graph, getResource(graph, s)) + ", " + NameUtils.getSafeName(graph, getResource(graph, p)) + "," + NameUtils.getSafeName(graph, getResource(graph, o)) + ")");
                                                }
-                                               
+
                                        }
                                } else {
                                        System.err.println("excluding shared " + s);
index b7fe6ed7b29f4cf3c9b45358e13eb9f32544dc31..9832f9d08be6815f2aaa6c24f6e0d64910a54e22 100644 (file)
@@ -81,7 +81,8 @@ public class ModelTransferableGraphSourceRequest extends UniqueRead<ModelTransfe
 
        public static String LOG_FILE = "transferableGraph.log";
        final static boolean LOG = false;
-       final static private boolean DEBUG = false;
+       final static boolean PRINTDEBUG = false;
+       final static boolean DEBUG = LOG | PRINTDEBUG;
        final static boolean PROFILE = false;
        
        private TransferableGraphConfiguration2 configuration;
@@ -103,8 +104,10 @@ public class ModelTransferableGraphSourceRequest extends UniqueRead<ModelTransfe
        }
        
        static void log(String line) {
+               if (PRINTDEBUG) System.err.println(line);
                if (LOG) {
                        try {
+                               if(line.length() > 500) line = line.substring(0, 500);
                                log.writeUTF(line + "\n");
                        } catch (IOException e) {
                                e.printStackTrace();
diff --git a/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/Subgraphs.java b/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/Subgraphs.java
deleted file mode 100644 (file)
index 518efc8..0000000
+++ /dev/null
@@ -1,2130 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2007, 2010 Association for Decentralized Information Management
- * in Industry THTH ry.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- *     VTT Technical Research Centre of Finland - initial API and implementation
- *******************************************************************************/
-package org.simantics.db.layer0.util;
-
-import java.io.DataOutput;
-import java.io.DataOutputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.ObjectOutputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-import java.util.concurrent.ConcurrentLinkedQueue;
-import java.util.concurrent.ConcurrentSkipListSet;
-
-import org.simantics.databoard.Bindings;
-import org.simantics.databoard.Databoard;
-import org.simantics.databoard.binding.Binding;
-import org.simantics.databoard.binding.mutable.Variant;
-import org.simantics.databoard.serialization.Serializer;
-import org.simantics.databoard.type.Datatype;
-import org.simantics.db.AsyncReadGraph;
-import org.simantics.db.DirectStatements;
-import org.simantics.db.ReadGraph;
-import org.simantics.db.Resource;
-import org.simantics.db.Statement;
-import org.simantics.db.common.request.AsyncReadRequest;
-import org.simantics.db.common.request.ReadRequest;
-import org.simantics.db.common.request.ResourceAsyncRead;
-import org.simantics.db.common.utils.NameUtils;
-import org.simantics.db.exception.DatabaseException;
-import org.simantics.db.layer0.adapter.SubgraphAdvisor;
-import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.layer0.util.ConsistsOfProcess.InternalEntry;
-import org.simantics.db.procedure.AsyncProcedure;
-import org.simantics.db.request.AsyncRead;
-import org.simantics.db.service.ClusteringSupport;
-import org.simantics.db.service.CollectionSupport;
-import org.simantics.db.service.DirectQuerySupport;
-import org.simantics.db.service.QueryControl;
-import org.simantics.db.service.QueryControl.ControlProcedure;
-import org.simantics.db.service.SerialisationSupport;
-import org.simantics.db.service.StatementSupport;
-import org.simantics.db.service.TransferableGraphSupport;
-import org.simantics.graph.representation.Extensions;
-import org.simantics.layer0.Layer0;
-import org.simantics.utils.datastructures.Pair;
-import org.simantics.utils.threads.logger.ITask;
-import org.simantics.utils.threads.logger.ThreadLogger;
-
-import gnu.trove.list.array.TIntArrayList;
-import gnu.trove.map.hash.TIntIntHashMap;
-import gnu.trove.map.hash.TLongObjectHashMap;
-import gnu.trove.procedure.TIntProcedure;
-import gnu.trove.procedure.TLongObjectProcedure;
-import gnu.trove.set.TIntSet;
-import gnu.trove.set.hash.THashSet;
-import gnu.trove.set.hash.TIntHashSet;
-
-public class Subgraphs {
-
-       public static String LOG_FILE = "export.log";
-       final static private boolean LOG = false;
-       final static private boolean DEBUG = false;
-       final static private boolean PARENT_DEBUG = DEBUG | false;
-       final static private boolean EXTERNAL_DEBUG = DEBUG | false;
-       final static private boolean ADVISOR_LOG = LOG & false;
-       final static private boolean EXPANSION_LOG = LOG & false;
-       final static private boolean INTERNAL_LOG = LOG & false;
-       final static private boolean COMPOSED_LOG = LOG & false;
-       final static private boolean RESOLVE_LOG = LOG & false;
-       final static private boolean CLASSIFY_LOG = LOG & false;
-       final static private boolean EXTERNAL_LOG = LOG & false;
-       final static private boolean PROFILE = false;
-
-       static enum WeakStatus {
-               STRONG, WEAK
-       }
-
-       
-       static DataOutput log;
-
-       static {
-
-               if (LOG) {
-                       try {
-                               FileOutputStream stream = new FileOutputStream(LOG_FILE, false);
-                               log = new DataOutputStream(stream);
-                       } catch (FileNotFoundException e) {
-                               e.printStackTrace();
-                       }
-               }
-
-       }
-       
-       private static void log(String line) {
-               if (LOG) {
-                       try {
-                               log.write((line + "\n").getBytes());
-                       } catch (IOException e) {
-                               e.printStackTrace();
-                       }
-               }
-       }
-
-       public static Collection<Resource> getParents(ReadGraph g, Resource r)
-                       throws DatabaseException {
-               return getParents(g, r, false);
-       }
-
-       static class FastInternalRequest extends ResourceAsyncRead<Boolean> {
-
-               final DirectQuerySupport dqs;
-               final ConcurrentLinkedQueue<Resource> queue;
-               final Map<Resource, WeakStatus> weakInverses;
-               final Map<Resource, ExtentStatus> status;
-
-               public FastInternalRequest(DirectQuerySupport dqs, Resource resource,
-                               Map<Resource, ExtentStatus> status,
-                               Map<Resource, WeakStatus> weakInverses,
-                               ConcurrentLinkedQueue<Resource> queue) {
-                       super(resource);
-                       this.dqs = dqs;
-                       this.status = status;
-                       this.weakInverses = weakInverses;
-                       this.queue = queue;
-               }
-
-               @Override
-               public int getFlags() {
-                       return 0;
-               }
-
-               @Override
-               public void perform(AsyncReadGraph graph, final AsyncProcedure<Boolean> procedure) {
-
-                       dqs.forEachDirectStatement(graph, resource, new AsyncProcedure<DirectStatements>() {
-
-                               @Override
-                               public void execute(AsyncReadGraph graph, DirectStatements ss) {
-                                       boolean ok = true;
-                                       for(Statement statement : ss) {
-                                               if (status.get(statement.getObject()) == ExtentStatus.INTERNAL) continue;
-                                               WeakStatus status = weakInverses.get(statement.getPredicate()); 
-                                               if(status == WeakStatus.WEAK) continue;
-                                               else if (status == null) {
-                                                       queue.add(statement.getPredicate());
-                                               }
-                                               ok = false;
-                                       }
-                                       procedure.execute(graph, ok);
-                               }
-
-                               @Override
-                               public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                       throwable.printStackTrace();
-                               }
-
-                       });
-                       
-               }
-
-       }
-
-       static class ClassifyStatementsRequest implements AsyncRead<Boolean> {
-
-               final Set<Resource> schedule;
-               final Map<Resource, WeakStatus> weakMap;
-
-               public ClassifyStatementsRequest(Set<Resource> schedule, Map<Resource, WeakStatus> weakMap) {
-                       this.weakMap = weakMap;
-                       this.schedule = schedule;
-               }
-
-           @Override
-           public int threadHash() {
-               return hashCode();
-           }
-               
-               @Override
-               public int getFlags() {
-                       return 0;
-               }
-
-               @Override
-               public void perform(AsyncReadGraph graph, final AsyncProcedure<Boolean> procedure) {
-
-                       for (final Resource p : schedule) {
-
-                               graph.forPossibleInverse(p, new AsyncProcedure<Resource>() {
-
-                                       private void register(AsyncReadGraph graph, Resource predicate, Resource superRelation, WeakStatus status) {
-                                               synchronized (weakMap) {
-                                                       weakMap.put(predicate, status);
-                                                       if(superRelation != null) weakMap.put(superRelation, status);
-                                               }
-                                       }
-
-                                       @Override
-                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                               throwable.printStackTrace();
-                                       }
-
-                                       @Override
-                                       public void execute(AsyncReadGraph graph, final Resource inverse) {
-
-                                               if (inverse == null) {
-                                                       
-                                                       register(graph, p, null, WeakStatus.WEAK);
-                                                       
-                                               } else {
-                                                       
-                                                       graph.forPossibleSuperrelation(inverse, new AsyncProcedure<Resource>() {
-
-                                                               @Override
-                                                               public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                                       throwable.printStackTrace();
-                                                               }
-
-                                                               @Override
-                                                               public void execute(AsyncReadGraph graph, final Resource superRelation) {
-                                                                       
-                                                                       if(superRelation != null && weakMap.containsKey(superRelation)) {
-                                                                               register(graph, p, null, weakMap.get(superRelation));
-                                                                               return;
-                                                                       }
-
-                                                                       graph.forIsSubrelationOf(inverse, graph.getService(Layer0.class).IsRelatedTo, new AsyncProcedure<Boolean>() {
-
-                                                                               @Override
-                                                                               public void exception(AsyncReadGraph graph,Throwable throwable) {
-                                                                                       throwable.printStackTrace();
-                                                                               }
-
-                                                                               @Override
-                                                                               public void execute(AsyncReadGraph graph,Boolean strong) {
-                                                                                       register(graph, p, superRelation, strong ? WeakStatus.STRONG : WeakStatus.WEAK);
-                                                                               }
-
-                                                                       });
-                                                                       
-                                                               }
-                                                               
-                                                       });
-                                                       
-                                               }
-
-                                       }
-
-                               });
-
-                       }
-
-                       procedure.execute(graph, false);
-
-               }
-
-       }
-
-       private static Collection<Resource> getParents(ReadGraph g, Resource r, boolean isStrong) throws DatabaseException {
-
-               System.out.println("getParents " + NameUtils.getSafeName(g, r));
-
-               Layer0 l0 = Layer0.getInstance(g);
-
-               Collection<Resource> predicates = g.getPredicates(r);
-
-               // --- Consists Of ----------------------------------------------------
-
-               if (predicates.contains(l0.PartOf)) {
-                       Collection<Resource> parents = g.getObjects(r, l0.PartOf);
-                       if (parents.size() == 1)
-                               return parents;
-                       ArrayList<Resource> libraryParents = new ArrayList<Resource>(1);
-                       for (Resource p : parents)
-                               if (g.isInstanceOf(p, l0.Library))
-                                       libraryParents.add(p);
-                       if (!libraryParents.isEmpty())
-                               return libraryParents;
-                       else
-                               return parents;
-               }
-
-               // --- Ordered sets ---------------------------------------------------
-
-               {
-                       Collection<Resource> parents = null;
-                       for (Resource p : predicates)
-                               if (g.isInstanceOf(p, l0.OrderedSet) && !p.equals(r)) {
-                                       if (parents == null)
-                                               parents = new ArrayList<Resource>(1);
-                                       parents.add(p);
-                               }
-                       if (parents != null) {
-                               if (DEBUG)
-                                       System.out.println("ORDERED SET");
-                               return parents;
-                       }
-               }
-
-
-               if (isStrong)
-                       return Collections.emptyList();
-               else {
-
-                       if (predicates.contains(l0.InverseOf)) {
-                               
-                               Resource inv = g.getInverse(r);
-                               return getParents(g, inv, true);
-                               
-                       } else {
-                               
-                               /*
-                                * Depends On
-                                * 
-                                * If there are DependsOn parents, then IsRelatedTo parents are discarded
-                                * 
-                                */
-                               HashSet<Resource> result = new HashSet<Resource>();
-                               for(Resource predicate : predicates) {
-                                       if(g.isSubrelationOf(predicate, l0.IsDependencyOf)) result.addAll(g.getObjects(r, predicate));
-                               }
-                               if(!result.isEmpty()) return result;
-                               
-                               /*
-                                * Is Related To
-                                * 
-                                * At this point all Is Related To are parents.
-                                * 
-                                */
-                               for(Resource predicate : predicates) {
-                                       Resource inv = g.getPossibleInverse(predicate);
-                                       if(inv != null) {
-                                               if(g.isSubrelationOf(inv, l0.IsRelatedTo)) result.addAll(g.getObjects(r, predicate)); 
-                                       }
-                               }
-                               
-                               return result;
-                               
-                       }
-                       
-                       /*
-                       Collection<Resource> invR = g.getObjects(r, b.IsRelatedTo_Inverse);
-                       if (predicates.contains(b.InverseOf)) {
-                               if (invR.size() > 1) {
-                                       if (DEBUG)
-                                               System.out
-                                                               .println("###########################################");
-                                       Resource inv = g.getInverse(r);
-                                       Collection<Resource> ret = new ArrayList<Resource>();
-                                       for (Statement pp : g.getStatements(r,
-                                                       b.IsRelatedTo_Inverse))
-                                               if (!pp.getPredicate().equals(inv)) {
-                                                       if (DEBUG) {
-                                                               System.out.println("<"
-                                                                               + NameUtils.getSafeName(g, pp
-                                                                                               .getSubject())
-                                                                               + ","
-                                                                               + NameUtils.getSafeName(g, pp
-                                                                                               .getPredicate())
-                                                                               + ","
-                                                                               + NameUtils.getSafeName(g, pp
-                                                                                               .getObject()) + ">");
-                                                       }
-                                                       ret.add(pp.getObject());
-                                               }
-                                       return ret;
-                               }
-                               // System.out.println("?????????????????");
-                               Collection<Resource> invParents = getParents(g,
-                                               g.getInverse(r), true);
-                               if (!invParents.isEmpty())
-                                       return invParents;
-                       }
-                       if (DEBUG) {
-                               System.out.print("invR");
-                               for (Resource res : invR)
-                                       System.out.print(" " + NameUtils.getSafeName(g, res));
-                               System.out.println();
-                       }
-                       return invR;
-                       */
-               }
-
-       }
-
-//     public static String getIdentifier(ReadGraph g, Resource r)
-//                     throws DatabaseException {
-//     Layer0 L0 = Layer0.getInstance(g);
-//             if (r.equals(g.getRootLibrary()))
-//                     return "";
-//             String name = g.getPossibleRelatedValue(r, L0.HasName);
-//             if (name == null)
-//                     return null;
-//             Collection<Resource> parents = getParents(g, r, true);
-//             if (parents.size() != 1)
-//                     return null;
-//             for (Resource p : parents) {
-//                     String parentIdentifier = getIdentifier(g, p);
-//                     if (parentIdentifier == null)
-//                             return null;
-//                     return parentIdentifier + "/" + name;
-//             }
-//             return null;
-//     }
-
-       static int kess = 0;
-
-       static class Expansion extends AsyncReadRequest {
-
-               final private Collection<Resource> roots;
-               final Collection<DirectStatements>[] results;
-               final Collection<Resource>[] listElements;
-               
-               public Expansion(Collection<Resource> roots, Collection<DirectStatements>[] results, Collection<Resource>[] listElements) {
-                       this.roots = roots;
-                       this.results = results;
-                       this.listElements = listElements;
-               }
-
-               @Override
-               public void run(AsyncReadGraph graph) {
-
-                       QueryControl control = graph.getService(QueryControl.class);
-                       final DirectQuerySupport dqs = graph.getService(DirectQuerySupport.class);
-
-                       final DomainStatementProcedure proc = new DomainStatementProcedure(dqs, graph.getService(StatementSupport.class), graph.getService(Layer0.class), results, listElements);
-
-                       int slice = (int) (roots.size() / control.getAmountOfQueryThreads()) + 1;
-
-                       final Resource[] rootArray = roots.toArray(Resource.NONE);
-                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-
-                               final int start = i * slice;
-                               final int end = Math.min(start + slice, rootArray.length);
-
-                               control.schedule(graph, i, new ControlProcedure() {
-
-                                       @Override
-                                       public void execute(AsyncReadGraph graph) {
-                                               for (int index = start; index < end; index++) {
-                                                       dqs.forEachDirectStatement(graph, rootArray[index], proc);
-                                               }
-
-                                       }
-
-                               });
-
-                       }
-
-               }
-
-               @Override
-               public int getFlags() {
-                       return 0;
-               }
-
-       }
-
-       static class Expansion2 extends AsyncReadRequest {
-
-               final private Collection<Resource> roots;
-               final Collection<DirectStatements>[] results;
-               final boolean ignoreVirtual;
-
-               public Expansion2(Collection<Resource> roots, Collection<DirectStatements>[] results) {
-                       this(roots, results, true);
-               }
-
-               public Expansion2(Collection<Resource> roots, Collection<DirectStatements>[] results, boolean ignoreVirtual) {
-                       this.roots = roots;
-                       this.results = results;
-                       this.ignoreVirtual = ignoreVirtual;
-               }
-
-               @Override
-               public void run(AsyncReadGraph graph) {
-
-                       QueryControl control = graph.getService(QueryControl.class);
-                       final DirectQuerySupport dqs = graph.getService(DirectQuerySupport.class);
-
-                       final DomainStatementProcedure2 proc = 
-                               new DomainStatementProcedure2(results);
-
-                       int slice = (int) (roots.size() / control.getAmountOfQueryThreads()) + 1;
-
-                       final Resource[] rootArray = roots.toArray(Resource.NONE);
-                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-
-                               final int start = i * slice;
-                               final int end = Math.min(start + slice, rootArray.length);
-
-                               control.schedule(graph, i, new ControlProcedure() {
-                                       @Override
-                                       public void execute(AsyncReadGraph graph) {
-                                               if (ignoreVirtual) {
-                                                       for (int index = start; index < end; index++) {
-                                                               dqs.forEachDirectPersistentStatement(graph, rootArray[index], proc);
-                                                       }
-                                               } else {
-                                                       for (int index = start; index < end; index++) {
-                                                               dqs.forEachDirectStatement(graph, rootArray[index], proc);
-                                                       }
-                                               }
-                                       }
-                               });
-
-                       }
-
-               }
-
-               @Override
-               public int getFlags() {
-                       return 0;
-               }
-
-       }
-       
-       static class DomainProcessor2 {
-
-               Serializer variantSerializer;
-
-               int id = 0;
-
-               Set<Resource> fringe = null;
-               Set<Resource> exclusions = new HashSet<Resource>();
-               Set<Resource> internalDomain = new HashSet<Resource>();
-               Set<Resource> sharedExternalReferences = null;
-               TIntSet sharedExternalIds = null;
-               Set<Resource> sharedExternalFringe = null;
-               Set<Resource> predicates = null;
-               Set<Resource> isRelatedToPredicates = null;
-               Set<Resource> sharedPredicates = null;
-               TIntIntHashMap ids = null;
-               Map<Resource, Statement> specials = null;
-               Map<Resource, ExtentStatus> status = null;
-               Map<Resource, WeakStatus> weakInverses = null;
-               
-//             final ArrayList<Double> priorityList = new ArrayList<Double>();
-
-               private long composedObjectCounter = 0;
-               private long fastInternalCounter = 0;
-               private long parentExternalCounter = 0;
-               private long fullInternalCounter = 0;
-               private long fullExternalCounter = 0;
-
-               private long startupTime = 0;
-               private long expandTime = 0;
-               private long fullResolveTime = 0;
-               private long fastResolveTime = 0;
-               private long otherStatementTime = 0;
-               private long parentResolveTime = 0;
-               private long extentSeedTime = 0;
-               private long composedPredicateTime = 0;
-               private long composedObjectTime = 0;
-
-               public void expand(ReadGraph graph, Set<Resource> fringe, Collection<DirectStatements>[] expansion) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       Collection<Collection<DirectStatements>[]> fullExpansion = new ArrayList<Collection<DirectStatements>[]>();
-                       QueryControl control = graph.getService(QueryControl.class);
-                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-                               expansion[i] = new ArrayList<DirectStatements>();
-                       }
-                       
-                       graph.syncRequest(new Expansion2(fringe, expansion));
-
-                       fringe.clear();
-
-                       expandTime += (System.nanoTime() - start);
-
-               }
-
-               public void classifyPredicates(ReadGraph graph, final Set<Resource> schedule) throws DatabaseException {
-
-                       CollectionSupport cs = graph.getService(CollectionSupport.class);
-
-                       final Layer0 L0 = Layer0.getInstance(graph);
-                       
-                       long start = System.nanoTime();
-
-                       final ConcurrentLinkedQueue<Resource> composedResult = new ConcurrentLinkedQueue<Resource>();
-                       final ConcurrentLinkedQueue<Resource> singleResult = new ConcurrentLinkedQueue<Resource>();
-                       final ConcurrentLinkedQueue<Resource> sharedResult = new ConcurrentLinkedQueue<Resource>();
-                       final ConcurrentLinkedQueue<Pair<Resource, Resource>> singles = new ConcurrentLinkedQueue<Pair<Resource, Resource>>();
-
-                       // Discover singles
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : schedule) {
-                                               
-                                               graph.forPossibleSuperrelation(predicate, new AsyncProcedure<Resource>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, final Resource single) {
-                                                               singles.add(Pair.make(predicate, single));
-                                                       }
-
-                                               });
-
-                                               graph.forHasStatement(predicate, L0.SharedRange, new AsyncProcedure<Boolean>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, final Boolean shared) {
-                                                               if(shared) sharedResult.add(predicate);
-                                                       }
-
-                                               });
-                                               
-                                       }
-
-                               }
-                               
-                       });
-
-                       // Determine singles
-                       final Set<Resource> singleSchedule = cs.createSet();
-                       for(Pair<Resource, Resource> pair : singles) {
-                               
-                               Resource single = pair.second;
-                               if(single != null && predicates.add(single)) singleSchedule.add(single);
-                               
-                       }
-                       
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : singleSchedule) {
-
-                                               graph.forIsSubrelationOf(predicate, L0.IsRelatedTo, new AsyncProcedure<Boolean>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, Boolean strong) {
-                                                               if (strong) singleResult.add(predicate);
-                                                       }
-
-                                               });
-                                               
-                                       }
-
-                               }
-                               
-                       });
-
-                       isRelatedToPredicates.addAll(singleResult);
-                       sharedPredicates.addAll(sharedResult);
-
-                       final Set<Resource> specialSchedule = cs.createSet();
-                       
-                       // Classify
-                       for(Pair<Resource, Resource> pair : singles) {
-                               
-                               Resource single = pair.second;
-                               if(single != null) {
-                                       if(isRelatedToPredicates.contains(single)) {
-                                               isRelatedToPredicates.add(pair.first);
-                                       }
-                               } else {
-                                       specialSchedule.add(pair.first);
-                               }
-                               
-                       }
-                       
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : specialSchedule) {
-
-                                               graph.forIsSubrelationOf(predicate, L0.IsRelatedTo, new AsyncProcedure<Boolean>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, Boolean composed) {
-                                                               if (composed) composedResult.add(predicate);
-                                                       }
-
-                                               });
-                                               
-                                       }
-
-                               }
-                               
-                       });
-                       
-                       isRelatedToPredicates.addAll(composedResult);
-
-                       composedPredicateTime += (System.nanoTime() - start);
-                       
-               }
-               
-               private Set<Resource> strongInverseSet = new HashSet<Resource>();
-
-               public void classifyPredicates(ReadGraph graph, final Collection<DirectStatements>[] expansion) throws DatabaseException {
-
-                       CollectionSupport cs = graph.getService(CollectionSupport.class);
-                       final Set<Resource> schedule = cs.createSet();
-                       final Map<Resource, Resource> newPredicates = cs.createMap(Resource.class);
-                       
-                       for (Collection<DirectStatements> coll : expansion)
-                               for (DirectStatements stms : coll)
-                                       for(Statement stm : stms) {
-                                               
-                                               Resource predicate = stm.getPredicate();
-                                               
-                                               if(predicates.add(predicate)) {
-                                                       Resource inverse = graph.getPossibleInverse(predicate);
-                                                       schedule.add(predicate);
-                                                       if(inverse != null) {
-                                                               newPredicates.put(predicate, inverse);
-                                                               if(predicates.add(inverse)) schedule.add(inverse);
-                                                       }
-                                                       
-                                               }
-                                               
-                                       }
-
-                       classifyPredicates(graph, schedule);
-
-                       for(Map.Entry<Resource, Resource> entry : newPredicates.entrySet()) {
-                               // Inverse is strong => this has strong inverse
-                               if(isRelatedToPredicates.contains(entry.getValue())) {
-                                       strongInverseSet.add(entry.getKey());
-                               }
-                               // This is strong => inverse has strong inverse
-                               if(isRelatedToPredicates.contains(entry.getKey())) {
-                                       strongInverseSet.add(entry.getValue());
-                               }
-                       }
-                       
-               }
-
-               /*
-                * Composed objects are internal. Mark them for expansion.
-                */
-
-               public void processFringe(ReadGraph graph, Collection<DirectStatements>[] expansion,
-                               ObjectOutputStream otherStatementsOutput, ObjectOutputStream valueOutput) throws DatabaseException, IOException {
-
-                       SerialisationSupport support = graph.getService(SerialisationSupport.class);
-                       TransferableGraphSupport tgs = graph.getService(TransferableGraphSupport.class);
-
-                       Layer0 L0 = Layer0.getInstance(graph);
-                       
-                       long start = System.nanoTime();
-                       
-                       for (Collection<DirectStatements> coll : expansion)
-                               for (DirectStatements stms : coll) {
-                                       
-                                       Resource subject = stms.getSubject();
-                                       
-                                       boolean partOf = false;
-                                       for(Statement stm : stms) {
-                                               Resource predicate = stm.getPredicate();
-                                               if(L0.PartOf.equals(predicate)) {
-                                                       partOf = true;
-                                                       break;
-                                               }
-                                       }
-                                       
-                                       ExtentStatus subjectStatus = status.get(subject);
-                                       if(LOG && subjectStatus != null) log("EXISTING STATUS FOR " + graph.getPossibleURI(subject) + " - " + subjectStatus);
-                                       if(subjectStatus == ExtentStatus.EXTERNAL) continue;
-                                       if(partOf && (subjectStatus == null) && graph.getPossibleURI(subject) != null) {
-                                               
-                                               status.put(subject, ExtentStatus.EXTERNAL);
-                                               if(LOG) {
-                                                       String uri = graph.getPossibleURI(subject);
-                                                       if(uri == null) log("[EXTERNAL]: No URI for " + subject);
-                                                       else log("[EXTERNAL] " + uri);
-                                               }
-
-                                               // Check for SharedRange statements
-                                               for(Statement stm : stms) {
-                                                       Resource predicate = stm.getPredicate();
-                                                       if(sharedPredicates.contains(predicate)) {
-                                                               sharedExternalFringe.add(stm.getObject());
-                                                               if(LOG) {
-                                                                       log("[SHARED EXTERNAL FRINGE]: " + NameUtils.getSafeName(graph, stm.getObject()));
-                                                               }
-                                                       }
-                                               }
-                                               
-                                       } else {
-                                               
-                                               boolean special = specials.containsKey(subject);
-                                               if(LOG) {
-                                                       if(special) {
-                                                               log("[SPECIAL] " + NameUtils.getSafeName(graph, subject));
-                                                       }
-                                               }
-                                               
-                                               status.put(subject, ExtentStatus.INTERNAL);
-                                               if(LOG) log("[INTERNAL] " + NameUtils.getSafeName(graph, subject));
-
-                                               int sId = support.getTransientId(subject);
-
-                                               if(graph.hasValue(subject)) {
-                                                       Datatype dt = graph.getRelatedValue(subject, L0.HasDataType, Bindings.getBindingUnchecked(Datatype.class));
-                                                       Binding b = Bindings.getBinding(dt);
-                                                       Object _value = graph.getValue(subject, b);
-                                                       Variant variant = new Variant(b, _value);
-                                                       byte[] value = variantSerializer.serialize(variant);
-                                                       if(LOG) log("[VALUE] " + NameUtils.getSafeName(graph, subject));
-                                                       valueOutput.writeInt(sId);
-                                                       valueOutput.writeInt(value.length);
-                                                       assert (value.length > 0);
-                                                       valueOutput.write(value);
-                                               }
-                                               
-                                               TIntArrayList stream = new TIntArrayList();
-                                               
-                                               for(Statement stm : stms) {
-
-                                                       if(special) {
-                                                               
-//                                                             System.err.println("stm=" + stm + " special=" + specials.get(subject));
-                                                               
-                                                       }
-
-                                                       Resource predicate = stm.getPredicate();
-                                                       Resource object = stm.getObject();
-
-                                                       ExtentStatus objectStatus = status.get(object);
-
-                                                       // Strong predicate
-                                                       if (isRelatedToPredicates.contains(predicate) && (objectStatus !=  ExtentStatus.EXCLUDED)) {
-                                               
-                                                               int pId = support.getTransientId(predicate);
-                                                               int oId = support.getTransientId(object);
-                                                               
-                                                               if(LOG) {
-                                                                       String s = NameUtils.getSafeName(graph, subject);
-                                                                       String p = NameUtils.getSafeName(graph, predicate);
-                                                                       String o = NameUtils.getSafeName(graph, object);
-                                                                       log("related=" + s + " - " + p + " - " + o);
-                                                               }
-                                                               
-                                                               stream.add(pId);
-                                                               stream.add(oId);
-                                                               
-                                                               if(objectStatus == null)
-                                                                       fringe.add(object);
-                                                               
-                                                       } else {
-                                                               
-                                                               // Weak predicate
-                                                               if(objectStatus == ExtentStatus.INTERNAL) {
-
-                                                                       // The inverse is also weak (or there is no inverse)
-                                                                       if(!strongInverseSet.contains(predicate)) {
-
-                                                                               int pId = support.getTransientId(predicate);
-                                                                               int oId = support.getTransientId(object);
-                                                                               
-                                                                               stream.add(pId);
-                                                                               stream.add(oId);
-                                                                       
-                                                                               if(LOG) {
-                                                                                       String s = NameUtils.getSafeName(graph, subject);
-                                                                                       String p = NameUtils.getSafeName(graph, predicate);
-                                                                                       String o = NameUtils.getSafeName(graph, object);
-                                                                                       log("fully weak internal=" + s + " - " + p + " - " + o + " - " + objectStatus);
-                                                                               }
-                                                                               
-                                                                       } else {
-
-                                                                               if(LOG) {
-                                                                                       String s = NameUtils.getSafeName(graph, subject);
-                                                                                       String p = NameUtils.getSafeName(graph, predicate);
-                                                                                       String o = NameUtils.getSafeName(graph, object);
-                                                                                       log("strong inverse internals=" + s + " - " + p + " - " + o + " - " + objectStatus);
-                                                                               }
-                                                                               
-                                                                       }
-                                                                       
-                                                               } else {
-
-                                                                       if(special) {
-                                                                               
-//                                                                             System.err.println("stm=" + stm + " special=" + specials.get(subject));
-                                                                               
-                                                                               Statement spec = specials.get(subject);
-                                                                               
-                                                                               // This statement can be specially treated
-                                                                               if(stm.getPredicate().equals(spec.getPredicate()) && stm.getObject().equals(spec.getObject())) {
-
-                                                                                       int pId = support.getTransientId(predicate);
-                                                                                       int oId = support.getTransientId(object);
-                                                                                       
-                                                                                       if(LOG) {
-                                                                                               String s = NameUtils.getSafeName(graph, subject);
-                                                                                               String p = NameUtils.getSafeName(graph, predicate);
-                                                                                               String o = NameUtils.getSafeName(graph, object);
-                                                                                               log("special=" + s + " - " + p + " - " + o);
-                                                                                       }
-                                                                                       
-                                                                                       stream.add(pId);
-                                                                                       stream.add(oId);
-                                                                                       
-                                                                               }
-                                                                               
-                                                                       } else {
-                                                                       
-                                                                               if(LOG) {
-                                                                                       String s = NameUtils.getSafeName(graph, subject);
-                                                                                       String p = NameUtils.getSafeName(graph, predicate);
-                                                                                       String o = NameUtils.getSafeName(graph, object);
-                                                                                       log("weak with unknown object=" + s + " - " + p + " - " + o + " - " + objectStatus);
-                                                                               }
-                                                                               
-                                                                       }
-                                                                       
-                                                               }
-                                                               
-                                                       }
-                                                       
-                                               }
-                                               
-                                               if(!stream.isEmpty()) {
-                                                       otherStatementsOutput.writeInt(sId);
-                                                       otherStatementsOutput.writeInt(stream.size() / 2);
-                                                       for (int i = 0; i < stream.size(); i++)
-                                                               otherStatementsOutput.writeInt(stream.getQuick(i));
-                                               }
-                                               
-                                       }
-                       
-                               }
-
-                       composedObjectTime += System.nanoTime() - start;
-
-               }
-
-               public void process(ReadGraph graph,
-                               ObjectOutputStream otherStatementsOutput,
-                               ObjectOutputStream valueOutput)
-                               throws DatabaseException, IOException {
-
-                       this.variantSerializer = graph.getService(Databoard.class).getSerializerUnchecked(Bindings.VARIANT);
-
-                       QueryControl control = graph.getService(QueryControl.class);
-
-//                     System.err.println("Begin ConsistsOfProcess");
-                       
-                       /*
-                        * Browse all stm = (s, ConsistsOf, o)
-                        * � All internal URIs are found => from now on, if unidentified resource has PartOf it is external.
-             * � All s are internal
-             * � All o are internal
-             * � All stm are included
-                        */
-                       Pair<List<InternalEntry>,Set<Resource>> pair = ConsistsOfProcess.walk(graph, null, fringe, exclusions, true);
-                       List<InternalEntry> entries = pair.first;
-                       for(InternalEntry entry : entries) {
-                               Resource r = entry.resource;
-                               if (status.put(r, ExtentStatus.INTERNAL) == null) {
-                                       String URI = graph.getPossibleURI(r);
-                                       if(URI != null) log("URI INTERNAL " + URI);
-                                       else log("URI has no URI for " + r);
-                                       fringe.add(r);
-                                       internalDomain.add(r);
-                               }
-                       }
-                       
-                       for(Resource unnamedChild : pair.second) {
-                           if (status.put(unnamedChild, ExtentStatus.INTERNAL) == null) {
-                               fringe.add(unnamedChild);
-                           }
-                       }
-                       
-                       /*
-                        * This loop resolves the transitive closure of all p < IsRelatedTo such that p does not contain the SharedRange tag.
-                        * Such resources are guaranteed to be internal.
-                        */
-                       while(!fringe.isEmpty()) {
-
-//                             System.err.println("Process Fringe with " + fringe.size() + ".");
-
-                               Collection<DirectStatements>[] expansion = new ArrayList[control.getAmountOfQueryThreads()];
-
-//                             System.err.println("-expand");
-
-                               // Expand fringe
-                               expand(graph, fringe, expansion);
-
-                               /*
-                                * classify all p
-                                * -IsRelatedTo
-                                * -SharedRange
-                                * -Internal / External
-                                */
-                               
-//                             System.err.println("-classify");
-
-                               classifyPredicates(graph, expansion);
-
-                               /*
-                                * for stms in [stms] 
-                                *   if stms contains predicate PartOf => s is External
-                                *   else s is Internal
-                                *   for all stm=(s,p,o) in stms
-                                *     if p <R IsRelatedTo => stm is included
-                                *     Fringe <- o
-                                */
-
-//                             System.err.println("-process");
-
-                               processFringe(graph, expansion, otherStatementsOutput, valueOutput);
-                               
-                       }
-
-                       while(!sharedExternalFringe.isEmpty()) {
-
-                               Collection<DirectStatements>[] expansion = new ArrayList[control.getAmountOfQueryThreads()];
-                               expand(graph, sharedExternalFringe, expansion);
-                               
-                               for (Collection<DirectStatements> coll : expansion)
-                                       for (DirectStatements stms : coll) {
-
-                                               Resource subject = stms.getSubject();
-                                               ExtentStatus subjectStatus = status.get(subject);
-                                               
-                                               if(ExtentStatus.INTERNAL == subjectStatus) {
-
-                                                       if(internalDomain.contains(subject)) continue;
-                                                       
-                                                       status.put(subject, ExtentStatus.EXTERNAL);
-                                                       sharedExternalReferences.add(subject);
-
-                                                       if(LOG) {
-                                                               log("[SHARED EXTERNAL REFERENCE]: " + NameUtils.getSafeName(graph, subject));
-                                                       }
-                                                       
-                                                       for(Statement stm : stms) {
-                                                               Resource predicate = stm.getPredicate();
-                                                               if (isRelatedToPredicates.contains(predicate)) {
-                                                                       sharedExternalFringe.add(stm.getObject());
-                                                               }
-                                                       }
-                                                       
-                                               }
-                                       }
-                               
-                       }
-
-                       if (PROFILE) {
-                               System.out.println(composedObjectCounter + " " + fastInternalCounter
-                                               + " " + parentExternalCounter + " "
-                                               + fullExternalCounter + " " + fullInternalCounter);
-                       }
-
-               }
-
-       }
-
-       static class DomainProcessor {
-
-               Serializer variantSerializer;
-
-               int id = 0;
-
-               Set<Resource> predicates = null;
-               Set<Resource> composedPredicates = null;
-               Set<Resource> expansionSeeds = null;
-               Map<Resource, Integer> ids = null;
-               Map<Resource, ExtentStatus> status = null;
-               Map<Resource, WeakStatus> weakInverses = null;
-               
-               final Set<SubgraphAdvisor> advisors;
-               final ArrayList<Double> priorityList = new ArrayList<Double>();
-
-               private long composedObjectCounter = 0;
-               private long fastInternalCounter = 0;
-               private long parentExternalCounter = 0;
-               private long fullInternalCounter = 0;
-               private long fullExternalCounter = 0;
-
-               private long startupTime = 0;
-               private long expandTime = 0;
-               private long fullResolveTime = 0;
-               private long fastResolveTime = 0;
-               private long otherStatementTime = 0;
-               private long parentResolveTime = 0;
-               private long extentSeedTime = 0;
-               private long composedPredicateTime = 0;
-               private long composedObjectTime = 0;
-
-               public DomainProcessor(Set<SubgraphAdvisor> advisors) {
-                       this.advisors = advisors;
-                       HashSet<Double> prioritySet = new HashSet<Double>();
-                       for (SubgraphAdvisor advisor : advisors)
-                               prioritySet.add(advisor.priority());
-                       priorityList.addAll(prioritySet);
-                       Collections.sort(priorityList);
-               }
-
-               public void expand(ReadGraph graph, Collection<DirectStatements>[] expansion, Set<Resource> schedule) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-//                     if (DEBUG)
-//                             System.out.println("expanding " + expansionSeeds.size() + " resources.");
-
-                       QueryControl control = graph.getService(QueryControl.class);
-//                     final Collection<DirectStatements>[] results = new ArrayList[control.getAmountOfQueryThreads()];
-                       final ArrayList<Resource>[] listElements = new ArrayList[control.getAmountOfQueryThreads()];
-                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-//                             results[i] = new ArrayList<DirectStatements>();
-                               listElements[i] = new ArrayList<Resource>();
-                       }
-                       
-//                     if(DEBUG) {
-//                             for(Resource r : expansionSeeds)
-//                                     System.out.println("Expanding " + NameUtils.getSafeName(graph, r, true));
-//                     }
-                       
-                       graph.syncRequest(new Expansion(expansionSeeds, expansion, listElements));
-                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-//                             for (DirectStatements s : results[i]) {
-//                                     expansion.put(s.getSubject(), s);
-//                             }
-                               for (Resource s : listElements[i]) {
-                                       schedule.add(s);
-//                                     if(status.put(s, ExtentStatus.INTERNAL) == null) {
-//                                             ids.put(s, id++);
-//                                     }
-                               }
-                       }
-
-                       expandTime += (System.nanoTime() - start);
-
-               }
-
-               public void extractComposedPredicates(ReadGraph graph, final Collection<DirectStatements>[] expansion) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       CollectionSupport cs = graph.getService(CollectionSupport.class);
-                       
-                       final ConcurrentLinkedQueue<Resource> composedResult = new ConcurrentLinkedQueue<Resource>();
-                       final ConcurrentLinkedQueue<Resource> singleResult = new ConcurrentLinkedQueue<Resource>();
-                       final ConcurrentLinkedQueue<Pair<Resource, Resource>> singles = new ConcurrentLinkedQueue<Pair<Resource, Resource>>();
-                       
-                       final Set<Resource> schedule = cs.createSet();
-                       
-                       for (Collection<DirectStatements> coll : expansion)
-                               for (DirectStatements stms : coll)
-                                       for(Statement stm : stms) {
-                                               Resource predicate = stm.getPredicate();
-                                               if(predicates.add(predicate)) schedule.add(predicate);  
-                                       }
-
-                       // Discover singles
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : schedule) {
-                                               
-                                               graph.forPossibleSuperrelation(predicate, new AsyncProcedure<Resource>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, final Resource single) {
-                                                               singles.add(Pair.make(predicate, single));
-                                                       }
-
-                                               });
-
-                                       }
-
-                               }
-                               
-                       });
-
-                       // Determine singles
-                       final Set<Resource> singleSchedule = cs.createSet();
-                       for(Pair<Resource, Resource> pair : singles) {
-                               
-                               Resource single = pair.second;
-                               if(single != null && predicates.add(single)) singleSchedule.add(single);
-                               
-                       }
-                       
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : singleSchedule) {
-
-                                               graph.forIsSubrelationOf(predicate, graph.getService(Layer0.class).IsComposedOf, new AsyncProcedure<Boolean>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, Boolean composed) {
-                                                               if (composed) singleResult.add(predicate);
-                                                       }
-
-                                               });
-                                               
-                                       }
-
-                               }
-                               
-                       });
-
-                       composedPredicates.addAll(singleResult);
-
-                       final Set<Resource> specialSchedule = cs.createSet();
-                       
-                       // Classify
-                       for(Pair<Resource, Resource> pair : singles) {
-                               
-                               Resource single = pair.second;
-                               if(single != null) {
-                                       if(composedPredicates.contains(single)) {
-                                               composedPredicates.add(pair.first);
-                                       }
-                               } else {
-                                       specialSchedule.add(pair.first);
-                               }
-                               
-                       }
-                       
-                       graph.syncRequest(new AsyncReadRequest() {
-
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource predicate : specialSchedule) {
-
-                                               graph.forIsSubrelationOf(predicate, graph.getService(Layer0.class).IsComposedOf, new AsyncProcedure<Boolean>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, Boolean composed) {
-                                                               if (composed) composedResult.add(predicate);
-                                                       }
-
-                                               });
-                                               
-                                       }
-
-                               }
-                               
-                       });
-                       
-                       composedPredicates.addAll(composedResult);
-
-                       composedPredicateTime += (System.nanoTime() - start);
-
-               }
-
-               /*
-                * Composed objects are internal. Mark them for expansion.
-                */
-
-               public void collectComposedObjects(ReadGraph graph, Collection<DirectStatements>[] expansion, Set<Resource> typeTodo, Set<Resource> objectTodo,
-                               Set<Resource> predicateTodo) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       Layer0 l0 = Layer0.getInstance(graph);
-                       
-                       for (Collection<DirectStatements> coll : expansion)
-                               for (DirectStatements stms : coll)
-                                       for(Statement stm : stms) {
-
-                                               Resource predicate = stm.getPredicate();
-                                               Resource object = stm.getObject();
-                                               
-                                               if (composedPredicates.contains(predicate)) {
-                                                       
-                                                       ExtentStatus existing = status.put(object, ExtentStatus.INTERNAL);
-                                                       if(existing == null) {
-                                                               ids.put(object, id++);
-                                                               composedObjectCounter++;
-                                                               expansionSeeds.add(object);
-//                                                             System.err.println("internal: " + NameUtils.getSafeName(graph, object, true));
-                                                               if(LOG) log("[INTERNAL] (composed object) " + NameUtils.getSafeName(graph, object, true));
-                                                       } else if (existing == ExtentStatus.EXCLUDED) {
-                                                               System.err.println("preExcluded: " + NameUtils.getSafeName(graph, object, true));
-                                                               status.put(object, ExtentStatus.EXCLUDED);
-                                                       } else if (existing == ExtentStatus.EXTERNAL) {
-                                                               System.err.println("preExternal: " + NameUtils.getSafeName(graph, object, true));
-                                                               status.put(object, ExtentStatus.EXTERNAL);
-                                                       }
-                                                       
-                                               } else {
-
-//                                                     System.err.println("internal2: " + NameUtils.getSafeName(graph, object, true));
-                                                       
-                                                       if (!status.containsKey(object)) {
-                                                               if (l0.InstanceOf.equalsResource(predicate)) {
-                                                                       typeTodo.add(object);
-                                                               } else {
-                                                                       objectTodo.add(object);
-                                                               }
-                                                       }
-
-                                                       if (!status.containsKey(predicate)) {
-                                                               predicateTodo.add(predicate);
-                                                       }
-                                                       
-                                               }
-                                       }
-
-                       composedObjectTime += System.nanoTime() - start;
-
-               }
-
-               public void writeOtherStatements(ReadGraph graph, Collection<Collection<DirectStatements>[]> expansion, ObjectOutputStream composedStatementsOutput, ObjectOutputStream otherStatementsOutput,
-                               ObjectOutputStream valueOutput) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       Layer0 l0 = Layer0.getInstance(graph);
-                       SerialisationSupport support = graph.getService(SerialisationSupport.class);
-                       TransferableGraphSupport tgs = graph.getService(TransferableGraphSupport.class);
-
-                       TIntArrayList other = new TIntArrayList();
-                       TIntArrayList composed = new TIntArrayList();
-
-                       try {
-
-                               for (Collection<DirectStatements>[] colls : expansion)
-                                       for (Collection<DirectStatements> coll : colls)
-                                               for (DirectStatements stms : coll) {
-
-                                                       Resource subject = stms.getSubject();
-                                                       composed.resetQuick();
-
-                                                       int sId = support.getTransientId(subject);
-
-                                                       composedStatementsOutput.writeInt(sId);
-
-                                                       if(graph.hasValue(subject)) {
-                                                               Datatype dt = graph.getRelatedValue(subject, l0.HasDataType, Bindings.getBindingUnchecked(Datatype.class));
-                                                               Binding b = Bindings.getBinding(dt);
-                                                               Object _value = graph.getValue(subject, b);
-                                                               Variant variant = new Variant(b, _value);
-                                                               byte[] value = variantSerializer.serialize(variant);
-                                                               if(LOG) log("[VALUE] " + NameUtils.getSafeName(graph, subject));
-                                                               valueOutput.writeInt(sId);
-                                                               valueOutput.writeInt(value.length);
-                                                               assert (value.length > 0);
-                                                               valueOutput.write(value);
-                                                       }
-
-                                                       for (Statement s : stms) {
-
-                                                               Resource object = s.getObject();
-                                                               Resource predicate = s.getPredicate();
-
-                                                               ExtentStatus objectStatus = status.get(object); 
-                                                               
-                                                               if(objectStatus == ExtentStatus.INTERNAL) {
-                                                                       composed.add(support.getTransientId(predicate));
-                                                                       composed.add(support.getTransientId(object));
-                                                                       if(LOG) log("[COMPOSED] (internal object) " + NameUtils.toIdString(graph, s));
-                                                               } else if (l0.InstanceOf.equalsResource(predicate)) {
-                                                                       composed.add(support.getTransientId(predicate));
-                                                                       composed.add(support.getTransientId(object));
-                                                                       if(LOG) log("[COMPOSED] (instanceOf) " + NameUtils.toIdString(graph, s));
-                                                               } else if (l0.SubrelationOf.equalsResource(predicate)) {
-                                                                       composed.add(support.getTransientId(predicate));
-                                                                       composed.add(support.getTransientId(object));
-                                                                       if(LOG) log("[COMPOSED] (subrelationOf) " + NameUtils.toIdString(graph, s));
-                                                               } else {
-                                                                       if(objectStatus == ExtentStatus.EXTERNAL) {
-                                                                               if(DEBUG)
-                                                                                       System.out.println("other " + NameUtils.toIdString(graph, s));
-                                                                                       //System.out.println("other.add " + predicate + " - " + object);
-                                                                               other.add(support.getTransientId(predicate));
-                                                                               other.add(support.getTransientId(object));
-                                                                               if(LOG) log("[OTHER] (object is external) " + NameUtils.toIdString(graph, s));
-                                                                       }
-                                                               }
-
-                                                       }
-
-                                                       if(!other.isEmpty()) {
-                                                               otherStatementsOutput.writeInt(sId);
-                                                               otherStatementsOutput.writeInt(other.size() / 2);
-                                                               for (int i = 0; i < other.size(); i++)
-                                                                       otherStatementsOutput.writeInt(other.getQuick(i));
-                                                               other.resetQuick();
-                                                       }
-
-                                                       composedStatementsOutput.writeInt(composed.size() / 2);
-                                                       for (int i = 0; i < composed.size(); i++)
-                                                               composedStatementsOutput.writeInt(composed.getQuick(i));
-
-                                               }
-
-                       } catch (IOException e) {
-                               e.printStackTrace();
-                       }
-
-                       otherStatementTime += (System.nanoTime() - start);
-
-               }
-
-               boolean hasStrictParents(ReadGraph g, Resource r)
-                               throws DatabaseException {
-                       if (g.getPossibleURI(r) != null)
-                               return true;
-                       return false;
-               }
-
-               public boolean getExpansionSeedsFromExtents(ReadGraph graph, final Collection<DirectStatements>[] expansion) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       final ConcurrentLinkedQueue<Resource> accepts = new ConcurrentLinkedQueue<Resource>();
-
-                       /*
-                        * Determine statements which could accept statements with todo
-                        * objects
-                        */
-                       search: for (Double priority : priorityList) {
-                               
-                               for (final SubgraphAdvisor advisor : advisors) {
-                                       
-                                       if (advisor.priority() > 0)
-                                               continue;
-                                       
-                                       if (advisor.priority() == priority) {
-                                               
-                                               graph.syncRequest(new ReadRequest() {
-
-                                                       @Override
-                                                       public void run(ReadGraph graph) throws DatabaseException {
-
-                                                               for (Collection<DirectStatements> coll : expansion)
-                                                                       for (DirectStatements stms : coll)
-                                                                               for(final Statement stm : stms) {
-
-                                                                                       advisor.advise(graph, stm, new AsyncProcedure<Boolean>() {
-
-                                                                                               @Override
-                                                                                               public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                                                                       throwable.printStackTrace();
-                                                                                               }
-
-                                                                                               @Override
-                                                                                               public void execute(AsyncReadGraph graph, Boolean accept) {
-                                                                                                       if (accept) {
-                                                                                                               accepts.add(stm.getObject());
-                                                                                                       }
-                                                                                               }
-
-                                                                                       });
-
-                                                                               }
-
-                                                       }
-
-                                               });
-                                       }
-                                       if (!accepts.isEmpty())
-                                               break search;
-                               }
-                       }
-
-                       CollectionSupport cs = graph.getService(CollectionSupport.class);
-                       Set<Resource> schedule = cs.createSet();
-                       for (Resource r : accepts) {
-                               if(!status.containsKey(r))
-                                       schedule.add(r);
-                       }
-
-                       extentSeedTime += (System.nanoTime() - start);
-
-                       if (schedule.isEmpty())
-                               return false;
-
-                       fastResolve(graph, schedule);
-                       uriResolve(graph, schedule);
-                       fullResolve(graph, schedule, "accepts");
-
-                       return true;
-
-               }
-
-               ConcurrentLinkedQueue<Resource> fastInternals = new ConcurrentLinkedQueue<Resource>();
-
-               public void fastResolve(ReadGraph graph, final Set<Resource> rs)
-                               throws DatabaseException {
-                       // This collects and resolves weaks
-                       if(fastResolveLoop(graph, rs))
-                               // Weaks are now resolved
-                               fastResolveLoop(graph, rs);
-               }
-
-               public boolean fastResolveLoop(ReadGraph graph, final Set<Resource> rs)
-                               throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       final ConcurrentLinkedQueue<Resource> weakSchedule = new ConcurrentLinkedQueue<Resource>();
-
-                       graph.syncRequest(new AsyncRead<Boolean>() {
-
-                           @Override
-                           public int threadHash() {
-                               return hashCode();
-                           }
-                               
-                               @Override
-                               public int getFlags() {
-                                       return 0;
-                               }
-
-                               @Override
-                               public void perform(AsyncReadGraph graph,
-                                               AsyncProcedure<Boolean> procedure) {
-
-                                       QueryControl control = graph.getService(QueryControl.class);
-                                       final DirectQuerySupport dqs = graph.getService(DirectQuerySupport.class);
-
-                                       int slice = (int) (rs.size() / control
-                                                       .getAmountOfQueryThreads()) + 1;
-
-                                       final Resource[] rootArray = rs.toArray(Resource.NONE);
-                                       for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-
-                                               final int start = i * slice;
-                                               final int end = Math.min(start + slice,
-                                                               rootArray.length);
-
-                                               control.schedule(graph, i, new ControlProcedure() {
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph) {
-
-                                                               for (int index = start; index < end; index++) {
-
-                                                                       final Resource r = rootArray[index];
-
-                                                                       //if (status.containsKey(r)) continue;
-
-                                                                       graph.asyncRequest(new FastInternalRequest(dqs, r, status, weakInverses, weakSchedule),new AsyncProcedure<Boolean>() {
-
-                                                                               @Override
-                                                                               public void exception(AsyncReadGraph graph,Throwable throwable) {
-                                                                                       throwable.printStackTrace();
-                                                                               }
-
-                                                                               @Override
-                                                                               public void execute(AsyncReadGraph graph,Boolean isInternal) {
-                                                                                       if (isInternal) {
-                                                                                               fastInternals.add(r);
-                                                                                       }
-                                                                               }
-
-                                                                       });
-
-                                                               }
-
-                                                       }
-
-                                               });
-
-                                       }
-
-                                       procedure.execute(graph, true);
-
-                               }
-
-                       });
-
-                       if (!weakSchedule.isEmpty()) {
-                               THashSet<Resource> weaks = new THashSet<Resource>(weakSchedule);                                
-                               if (CLASSIFY_LOG)
-                                       for (Resource p : weakSchedule)
-                                               System.out.println("classify "
-                                                               + NameUtils.getSafeName(graph, p));
-                               graph.syncRequest(new ClassifyStatementsRequest(weaks, weakInverses));
-                       } 
-
-                       for (Resource r : fastInternals) {
-                               rs.remove(r);
-                               if (status.put(r, ExtentStatus.INTERNAL) == null) {
-                                       if(LOG) log("[INTERNAL] (fast) " + NameUtils.getSafeName(graph, r, true));
-                                       ids.put(r, id++);
-                                       fastInternalCounter++;
-                                       expansionSeeds.add(r);
-                               }
-                       }
-
-                       fastResolveTime += (System.nanoTime() - start);
-                       
-                       return !weakSchedule.isEmpty();                 
-
-               }
-
-               private ExtentStatus resolveExtent(ReadGraph graph, Resource r, Map<Resource, ExtentStatus> statuses, Set<Resource> expansionSeeds, THashSet<Resource> pending,
-                               ArrayList<Resource> stack) throws DatabaseException {
-
-                       ExtentStatus current = statuses.get(r);
-                       if(current != null) return current;
-                       
-                       if (pending.contains(r))
-                               return ExtentStatus.PENDING;
-
-                       // In order to break cyclic dependencies
-                       pending.add(r);
-
-                       if (PARENT_DEBUG)
-                               System.out.println("resolveExtent "
-                                               + NameUtils.getSafeName(graph, r));
-
-                       ExtentStatus status = ExtentStatus.INTERNAL;
-                       for (Resource p : getParents(graph, r)) {
-                               if (PARENT_DEBUG) {
-                                       ExtentStatus ps = statuses.get(p);
-                                       System.out.println(" parent " + NameUtils.getSafeName(graph, p) + "(" + ps + ")");
-                               }
-                               switch (resolveExtent(graph, p, statuses,
-                                               expansionSeeds, pending, stack)) {
-                               case EXTERNAL:
-                                       return ExtentStatus.EXTERNAL;
-                               case PENDING:
-                                       status = ExtentStatus.PENDING;
-                               }
-                       }
-                       if (status == ExtentStatus.INTERNAL) {
-                               pending.remove(r);
-                               stack.add(r);
-                               if (DEBUG)
-                                       System.out.println(NameUtils.getSafeName(graph, r, true)
-                                                       + " is internal.");
-                       }
-                       return status;
-               }
-
-               public void uriResolve(ReadGraph graph, final Set<Resource> todo)
-                               throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       for(Resource r : todo) System.out.println("uriResolve " +
-                                       NameUtils.getSafeName(graph, r));
-
-                       final ConcurrentSkipListSet<Resource> found = new ConcurrentSkipListSet<Resource>();
-
-                       graph.syncRequest(new AsyncReadRequest() {
-                               
-                               @Override
-                               public void run(AsyncReadGraph graph) {
-
-                                       for (final Resource r : todo) {
-
-                                               // System.out.println("uriresolve before " + r);
-
-                                               if (status.containsKey(r)) continue;
-
-                                               // System.out.println("uriresolve " + r);
-
-                                               graph.forURI(r, new AsyncProcedure<String>() {
-
-                                                       @Override
-                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                               throwable.printStackTrace();
-                                                       }
-
-                                                       @Override
-                                                       public void execute(AsyncReadGraph graph, String uri) {
-
-                                                               if (uri != null) {
-
-                                                                       // System.out.println("uriresolve has uri "
-                                                                       // + r);
-
-                                                                       if(found.add(r)) {
-                                                                               parentExternalCounter++;
-                                                                       }
-
-                                                               } else {
-
-                                                                       // System.out.println("uriresolve ask inverse "
-                                                                       // + r);
-
-                                                                       graph.forPossibleInverse(r, new AsyncProcedure<Resource>() {
-
-                                                                               @Override
-                                                                               public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                                                       throwable.printStackTrace();
-                                                                               }
-
-                                                                               @Override
-                                                                               public void execute(AsyncReadGraph graph, Resource inverse) {
-
-                                                                                       if (inverse != null) {
-
-                                                                                               graph.forURI(inverse, new AsyncProcedure<String>() {
-
-                                                                                                       @Override
-                                                                                                       public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                                                                               throwable.printStackTrace();
-                                                                                                       }
-
-                                                                                                       @Override
-                                                                                                       public void execute(AsyncReadGraph graph, String uri) {
-
-                                                                                                               if (uri != null) {
-
-                                                                                                                       if(found.add(r)) {
-                                                                                                                               parentExternalCounter++;
-                                                                                                                       }
-
-                                                                                                               }
-
-                                                                                                       }
-
-                                                                                               });
-
-                                                                                       }
-
-                                                                               }
-                                                                               
-                                                                       });
-
-                                                               }
-                                                       }
-
-                                               });
-
-                                       }
-
-                               }
-
-                       });
-
-                       todo.removeAll(found);
-                       for(Resource r : found) {
-                               status.put(r, ExtentStatus.EXTERNAL);
-                               if(LOG) log("[EXTERNAL] (uriResolve) " + NameUtils.getSafeName(graph, r, true));
-                       }
-                       
-                       parentResolveTime += System.nanoTime() - start;
-
-               }
-
-               public void fullResolve(ReadGraph graph, Collection<Resource> rs,
-                               String koss) throws DatabaseException {
-
-                       long start = System.nanoTime();
-
-                       for (final Resource r : rs) {
-
-                               if(status.containsKey(r)) continue;
-
-                               THashSet<Resource> pending = new THashSet<Resource>();
-                               ArrayList<Resource> stack = new ArrayList<Resource>();
-
-                               ExtentStatus s = resolveExtent(graph, r, status, expansionSeeds, pending, stack);
-                               if (ExtentStatus.INTERNAL == s || ExtentStatus.PENDING == s) {
-                                       if (status.put(r, ExtentStatus.INTERNAL) == null) {
-                                               if(LOG) log("[INTERNAL] (resolveExtent) " + NameUtils.getSafeName(graph, r, true));
-                                               ids.put(r, id++);
-                                               fullInternalCounter++;
-                                               expansionSeeds.add(r);
-                                       }
-                               }
-                               if (ExtentStatus.EXTERNAL == s) {
-                                       if (status.put(r, ExtentStatus.EXTERNAL) == null) {
-                                               if(LOG) log("[EXTERNAL] (resolveExtent) " + NameUtils.getSafeName(graph, r, true));
-                                               fullExternalCounter++;
-                                       }
-                               }
-
-                       }
-
-                       fullResolveTime += (System.nanoTime() - start);
-
-               }
-
-               public void process(ReadGraph graph,
-                               ObjectOutputStream composedStatementsOutput,
-                               ObjectOutputStream otherStatementsOutput,
-                               ObjectOutputStream valueOutput)
-                               throws DatabaseException {
-
-                       this.variantSerializer = graph.getService(Databoard.class).getSerializerUnchecked(Bindings.VARIANT);
-
-                       CollectionSupport cs = graph.getService(CollectionSupport.class);
-
-                       Set<Resource> typeTodo = cs.createSet();
-                       Set<Resource> objectTodo = cs.createSet();
-                       Set<Resource> predicateTodo = cs.createSet();
-                       
-                       Collection<Collection<DirectStatements>[]> fullExpansion = new ArrayList<Collection<DirectStatements>[]>();
-                       
-                       do {
-
-                               QueryControl control = graph.getService(QueryControl.class);
-                               Collection<DirectStatements>[] expansion = new ArrayList[control.getAmountOfQueryThreads()];
-                               for (int i = 0; i < control.getAmountOfQueryThreads(); i++) {
-                                       expansion[i] = new ArrayList<DirectStatements>();
-                               }
-                               
-                               // Expand expansionSeeds
-                               expand(graph, expansion, objectTodo);
-                               
-                               // Start collecting new seeds
-                               expansionSeeds = cs.createSet();
-
-                               // Collect predicates which are <R IsComposedOf
-                               extractComposedPredicates(graph, expansion);
-
-                               // Make composed objects internal and make sure they are further
-                               // expanded
-                               collectComposedObjects(graph, expansion, typeTodo, objectTodo, predicateTodo);
-
-                               /*
-                                * Use the expansion seed heuristic to find new resources to
-                                * expand before full analysis.
-                                */
-                               getExpansionSeedsFromExtents(graph, expansion);
-
-                               fullExpansion.add(expansion);
-
-                       } while (!expansionSeeds.isEmpty());
-
-                       fastResolve(graph, objectTodo);
-                       uriResolve(graph, predicateTodo);
-                       uriResolve(graph, objectTodo);
-                       uriResolve(graph, typeTodo);
-                       fullResolve(graph, objectTodo, "objectTodo");
-                       fullResolve(graph, predicateTodo, "predicateTodo");
-                       fullResolve(graph, typeTodo, "typeTodo");
-
-                       writeOtherStatements(graph, fullExpansion, composedStatementsOutput, otherStatementsOutput, valueOutput);
-
-                       if (PROFILE) {
-                               System.out.println(composedObjectCounter + " " + fastInternalCounter
-                                               + " " + parentExternalCounter + " "
-                                               + fullExternalCounter + " " + fullInternalCounter);
-                       }
-
-               }
-
-       }
-
-       public static void getDomain2(ReadGraph graph, TIntIntHashMap ids,
-                       Collection<Resource> roots, Map<Resource, ExtentStatus> preStatus,
-                       Map<Resource, Statement> specials,
-                       ObjectOutputStream otherStatementsOutput,
-                       ObjectOutputStream valueOutput,
-                       TreeMap<String, Variant> extensions,
-                       TIntHashSet excludedShared) throws DatabaseException {
-
-               ITask task = ThreadLogger.getInstance().begin("getDomain2");
-
-               final DomainProcessor2 processor = new DomainProcessor2();
-               
-               processor.startupTime = System.nanoTime();
-
-               Layer0 l0 = Layer0.getInstance(graph);
-               
-               CollectionSupport cs = graph.getService(CollectionSupport.class);
-               SerialisationSupport support = graph.getService(SerialisationSupport.class);
-
-               processor.ids = ids;
-               processor.specials = specials;
-               processor.status = cs.createMap(ExtentStatus.class);
-               processor.weakInverses = cs.createMap(WeakStatus.class);
-               processor.predicates = cs.createSet();
-               processor.isRelatedToPredicates = cs.createSet();
-               processor.sharedPredicates = cs.createSet();
-//             processor.expansionSeeds = cs.createSet();
-
-               for(Map.Entry<Resource, ExtentStatus> entry : preStatus.entrySet()) {
-                       processor.status.put(entry.getKey(), entry.getValue());
-                       if(ExtentStatus.EXCLUDED.equals(entry.getValue())) processor.exclusions.add(entry.getKey());
-               }
-               
-//             for (Resource r : excluded) {
-//                     processor.status.put(r, ExtentStatus.EXCLUDED);
-//             }
-               
-               Resource rootLibrary = graph.getResource("http:/");
-               
-               if (!roots.contains(rootLibrary))
-                       processor.status.put(rootLibrary, ExtentStatus.EXTERNAL);
-
-               for (Resource root : roots) {
-                       processor.status.put(root, ExtentStatus.INTERNAL);
-                       //processor.ids.put(support.getTransientId(root), processor.ids.size());
-                       for (Resource owner : graph.getObjects(root, l0.IsOwnedBy)) {
-                               processor.status.put(owner, ExtentStatus.EXTERNAL);
-                       }
-               }
-
-               processor.startupTime = System.nanoTime() - processor.startupTime;
-
-               processor.fringe = new HashSet<Resource>();
-               processor.fringe.addAll(roots);
-               
-               processor.internalDomain.addAll(roots);
-               
-               processor.sharedExternalReferences = new HashSet<Resource>();
-               processor.sharedExternalFringe = new HashSet<Resource>();
-
-               try {
-               
-                       processor.process(graph, otherStatementsOutput, valueOutput);
-               
-               } catch (IOException e) {
-                       e.printStackTrace();
-               }
-               
-               for(Resource r : processor.sharedExternalReferences) excludedShared.add(support.getTransientId(r));
-               
-       ClusteringSupport cls = graph.getService(ClusteringSupport.class);
-       TLongObjectHashMap<TIntArrayList> clusterMap = new TLongObjectHashMap<TIntArrayList>();
-               for(Map.Entry<Resource, ExtentStatus> entry : processor.status.entrySet()) {
-                       if(ExtentStatus.INTERNAL == entry.getValue()) {
-                               
-                               long cluster = cls.getCluster(entry.getKey());
-                               TIntArrayList list = clusterMap.get(cluster);
-                               if(list == null) {
-                                       list = new TIntArrayList();
-                                       clusterMap.put(cluster, list);
-                               }
-                               list.add(support.getTransientId(entry.getKey()));
-                               
-                       }
-               }
-               final TIntArrayList clustering = new TIntArrayList();
-               clusterMap.forEachEntry(new TLongObjectProcedure<TIntArrayList>() {
-                       
-                       @Override
-                       public boolean execute(long cluster, TIntArrayList b) {
-                               clustering.add(b.size());
-                               b.forEach(new TIntProcedure() {
-                                       
-                                       @Override
-                                       public boolean execute(int rId) {
-                                               processor.ids.put(rId, processor.id++);
-                                               return true;
-                                       }
-                                       
-                               });
-                               return true;
-                       }
-                       
-               });
-               
-               extensions.put(Extensions.CLUSTERING, new Variant(Bindings.INT_ARRAY, clustering.toArray()));
-               
-               long total = processor.startupTime + processor.expandTime
-                               + processor.composedPredicateTime
-                               + processor.composedObjectTime + processor.extentSeedTime
-                               + processor.fullResolveTime + processor.fastResolveTime + 
-                               + processor.parentResolveTime + processor.otherStatementTime;
-
-               if (PROFILE) {
-                       System.out.println("startup took " + 1e-9 * processor.startupTime
-                                       + "s.");
-                       System.out.println("expand took " + 1e-9 * processor.expandTime
-                                       + "s.");
-                       System.out.println("composedPredicates took " + 1e-9
-                                       * processor.composedPredicateTime + "s.");
-                       System.out.println("composedObjects took " + 1e-9
-                                       * processor.composedObjectTime + "s.");
-                       System.out.println("extentSeeding took " + 1e-9
-                                       * processor.extentSeedTime + "s.");
-                       System.out.println("fullResolve took " + 1e-9
-                                       * processor.fullResolveTime + "s.");
-                       System.out.println("fastResolve took " + 1e-9
-                                       * processor.fastResolveTime + "s.");
-                       System.out.println("parentResolve took " + 1e-9
-                                       * processor.parentResolveTime + "s.");
-                       System.out.println("otherStatements took " + 1e-9
-                                       * processor.otherStatementTime + "s.");
-                       System.out.println("total " + 1e-9 * total + "s.");
-               }
-
-               task.finish();
-
-               
-       }
-
-       
-       public static void getDomain(ReadGraph graph, Map<Resource, Integer> ids,
-                       Collection<Resource> roots, Map<Resource, ExtentStatus> preStatus, Set<SubgraphAdvisor> advisors,
-                       ObjectOutputStream composedStatementsOutput,
-                       ObjectOutputStream otherStatementsOutput,
-                       ObjectOutputStream valueOutput) throws DatabaseException {
-
-               ITask task = ThreadLogger.getInstance().begin("getDomain");
-
-               DomainProcessor processor = new DomainProcessor(advisors);
-               
-               processor.startupTime = System.nanoTime();
-
-               Layer0 l0 = Layer0.getInstance(graph);
-
-               CollectionSupport cs = graph.getService(CollectionSupport.class);
-
-               processor.ids = ids;
-               processor.status = cs.createMap(ExtentStatus.class);
-               processor.weakInverses = cs.createMap(WeakStatus.class);
-               processor.predicates = cs.createSet();
-               processor.composedPredicates = cs.createSet();
-               processor.expansionSeeds = cs.createSet();
-
-               for(Map.Entry<Resource, ExtentStatus> entry : preStatus.entrySet()) {
-                       processor.status.put(entry.getKey(), entry.getValue());
-               }
-
-//             for (Resource r : excluded) {
-//                     processor.status.put(r, ExtentStatus.EXCLUDED);
-//             }
-               
-               if (!roots.contains(graph.getRootLibrary()))
-                       processor.status.put(graph.getRootLibrary(), ExtentStatus.EXTERNAL);
-
-               for (Resource root : roots) {
-                       processor.status.put(root, ExtentStatus.INTERNAL);
-                       processor.ids.put(root, processor.id++);
-                       for (Resource owner : graph.getObjects(root, l0.IsOwnedBy)) {
-                               processor.status.put(owner, ExtentStatus.EXTERNAL);
-                       }
-               }
-
-
-               processor.expansionSeeds.addAll(roots);
-
-               processor.startupTime = System.nanoTime() - processor.startupTime;
-
-               while (!processor.expansionSeeds.isEmpty()) {
-
-                       processor.process(graph, composedStatementsOutput,
-                                       otherStatementsOutput, valueOutput);
-
-               }
-
-               long total = processor.startupTime + processor.expandTime
-                               + processor.composedPredicateTime
-                               + processor.composedObjectTime + processor.extentSeedTime
-                               + processor.fullResolveTime + processor.fastResolveTime + 
-                               + processor.parentResolveTime + processor.otherStatementTime;
-
-               if (PROFILE) {
-                       System.out.println("startup took " + 1e-9 * processor.startupTime
-                                       + "s.");
-                       System.out.println("expand took " + 1e-9 * processor.expandTime
-                                       + "s.");
-                       System.out.println("composedPredicates took " + 1e-9
-                                       * processor.composedPredicateTime + "s.");
-                       System.out.println("composedObjects took " + 1e-9
-                                       * processor.composedObjectTime + "s.");
-                       System.out.println("extentSeeding took " + 1e-9
-                                       * processor.extentSeedTime + "s.");
-                       System.out.println("fullResolve took " + 1e-9
-                                       * processor.fullResolveTime + "s.");
-                       System.out.println("fastResolve took " + 1e-9
-                                       * processor.fastResolveTime + "s.");
-                       System.out.println("parentResolve took " + 1e-9
-                                       * processor.parentResolveTime + "s.");
-                       System.out.println("otherStatements took " + 1e-9
-                                       * processor.otherStatementTime + "s.");
-                       System.out.println("total " + 1e-9 * total + "s.");
-               }
-
-               task.finish();
-
-       }
-
-}
index 350f4ca31d966b5bda61e7e570286e4488a8a0e6..4e23fa5750968ab64624843146da008ddc9ce9c9 100644 (file)
@@ -13,14 +13,15 @@ import org.simantics.db.common.request.PossibleIndexRoot;
 import org.simantics.db.common.utils.CommonDBUtils;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.layer0.util.TransferableGraphConfiguration2.RootSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.layer0.Layer0;
 
 public class TGConfigurer {
 
        final private ReadGraph graph;
-       final Collection<RootSpec> roots = new ArrayList<RootSpec>();
-       final Map<Resource, ExtentStatus> preStatus = new HashMap<Resource, ExtentStatus>();
+       final Collection<SeedSpec> roots = new ArrayList<>();
+       final Map<Resource, ExtentStatus> preStatus = new HashMap<>();
        final boolean ignoreVirtualResources;
        final boolean validate;
        
@@ -41,13 +42,12 @@ public class TGConfigurer {
                return this;
        }
 
-       public TGConfigurer roots(Collection<RootSpec> rs) throws DatabaseException {
+       public TGConfigurer roots(Collection<SeedSpec> rs) throws DatabaseException {
                Layer0 L0 = Layer0.getInstance(graph);
-               for(RootSpec root : rs) {
+               for(SeedSpec root : rs) {
                        Resource nameResource = graph.getPossibleObject(root.resource, L0.HasName);
                        if(nameResource != null) preStatus.put(nameResource, ExtentStatus.EXCLUDED);
-//                     String name = graph.getValue(nameResource, Bindings.STRING);
-                       roots.add(new RootSpec(root.resource, root.name, root.internal, root.type));
+                       roots.add(new SeedSpec(root.resource, root.name, root.specType, root.type));
                        preStatus.put(root.resource, ExtentStatus.INTERNAL);
                }
                return this;
@@ -63,7 +63,7 @@ public class TGConfigurer {
                                if(name == null) name = "<no name>";
                                preStatus.put(nameResource, ExtentStatus.EXCLUDED);
                        }
-                       roots.add(new RootSpec(root, name, true));
+                       roots.add(new SeedSpec(root, name, SeedSpecType.ROOT));
                        preStatus.put(root, ExtentStatus.INTERNAL);
                }
                return this;
@@ -73,8 +73,7 @@ public class TGConfigurer {
                Layer0 L0 = Layer0.getInstance(graph);
                for(NamedResource root : rs) {
                        Resource nameResource = graph.getPossibleObject(root.getResource(), L0.HasName);
-//                     String name = graph.getValue(nameResource, Bindings.STRING);
-                       roots.add(new RootSpec(root.getResource(), root.getName(), true));
+                       roots.add(new SeedSpec(root.getResource(), root.getName(), SeedSpecType.ROOT));
                        preStatus.put(root.getResource(), ExtentStatus.INTERNAL);
                        preStatus.put(nameResource, ExtentStatus.EXCLUDED);
                }
@@ -91,9 +90,9 @@ public class TGConfigurer {
 
                // -Exclude owners if not explicitly defined
                Layer0 L0 = Layer0.getInstance(graph);
-               ArrayList<Resource> rootList = new ArrayList<Resource>();
-               for (RootSpec root : roots) {
-                       if(root.internal) {
+               ArrayList<Resource> rootList = new ArrayList<>();
+               for (SeedSpec root : roots) {
+                       if(!SeedSpecType.SPECIAL_ROOT.equals(root.specType)) {
                                rootList.add(root.resource);
                                for (Resource owner : graph.getObjects(root.resource, L0.IsOwnedBy)) {
                                        ExtentStatus ownerStatus = preStatus.get(owner);
diff --git a/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TGConfigurer2.java b/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TGConfigurer2.java
new file mode 100644 (file)
index 0000000..f3758ae
--- /dev/null
@@ -0,0 +1,78 @@
+package org.simantics.db.layer0.util;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.simantics.db.ReadGraph;
+import org.simantics.db.Resource;
+import org.simantics.db.common.request.IsParent;
+import org.simantics.db.exception.DatabaseException;
+import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
+
+public class TGConfigurer2 {
+
+       final Collection<SeedSpec> seeds = new ArrayList<SeedSpec>();
+       final Map<Resource, ExtentStatus> preStatus = new HashMap<Resource, ExtentStatus>();
+       final boolean ignoreVirtualResources;
+       final boolean validate;
+
+       public TGConfigurer2(boolean ignoreVirtualResources, boolean validate) {
+               this.ignoreVirtualResources = ignoreVirtualResources;
+               this.validate = validate;
+       }
+
+       public TGConfigurer2 addInternalSeed(ReadGraph graph, Resource r) throws DatabaseException {
+
+               // If parent is already an internal => skip this
+               for(SeedSpec spec : seeds) {
+                       if(SeedSpecType.INTERNAL.equals(spec.specType)) {
+                               if(graph.syncRequest(new IsParent(spec.resource, r))) return this;
+                       }
+               }
+               // If some existing internal is a child of this one => remove them
+               List<Resource> removals = new ArrayList<>();
+               for(SeedSpec spec : seeds) {
+                       if(SeedSpecType.INTERNAL.equals(spec.specType)) {
+                               if(graph.syncRequest(new IsParent(r, spec.resource))) removals.add(spec.resource);
+                       }
+               }
+               for(Resource removal : removals) {
+                       SeedSpec spec = getSeed(removal);
+                       if(spec != null) {
+                               seeds.remove(spec);
+                       }
+               }
+
+               seeds.add(new SeedSpec(r, "", SeedSpecType.INTERNAL));
+
+               return this;
+
+       }
+
+       private SeedSpec getSeed(Resource r) {
+               for(SeedSpec spec : seeds) {
+                       if(spec.resource.equals(r)) return spec;
+               }
+               return null;
+       }
+
+       public TGConfigurer2 addExternal(Resource r) throws DatabaseException {
+               preStatus.put(r, ExtentStatus.EXTERNAL);
+               return this;
+       }
+
+       public TGConfigurer2 addExcluded(Resource r) throws DatabaseException {
+               preStatus.put(r, ExtentStatus.EXCLUDED);
+               return this;
+       }
+
+       public TransferableGraphConfiguration2 create() throws DatabaseException {
+               return new TransferableGraphConfiguration2(null, seeds, preStatus, ignoreVirtualResources, validate);
+       }
+
+}
index 0bd71af863fa4330b94b01969aff6e736c7c46b4..89da10f4493e738a0d61b32c5e6ff3271f81f903 100644 (file)
@@ -23,8 +23,9 @@ import org.simantics.db.Statement;
 import org.simantics.db.common.request.PossibleIndexRoot;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.adapter.impl.EntityInstances.QueryIndex;
-import org.simantics.db.layer0.util.ConsistsOfProcess.InternalEntry;
+import org.simantics.db.layer0.util.ConsistsOfProcess.ConsistsOfProcessEntry;
 import org.simantics.db.layer0.util.DomainProcessor3.ExclusionDecision;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
 import org.simantics.layer0.Layer0;
 import org.simantics.scl.runtime.function.Function1;
 import org.simantics.utils.datastructures.Pair;
@@ -65,9 +66,9 @@ public class TGRepresentationUtils {
                         return new GUIDExclusionFunction(graph);
 
                     // The root is OK - check everything beneath
-                    Pair<List<InternalEntry>,Set<Resource>> pair = ConsistsOfProcess.walk(graph, null, Collections.singleton(r), Collections.emptySet(), true); 
-                    List<InternalEntry> entries = pair.first;
-                    for(InternalEntry entry : entries) {
+                    Pair<List<ConsistsOfProcessEntry>,Set<Resource>> pair = ConsistsOfProcess.walk(graph, Collections.singleton(SeedSpec.internal(r)), true); 
+                    List<ConsistsOfProcessEntry> entries = pair.first;
+                    for(ConsistsOfProcessEntry entry : entries) {
                         if(findByIdentifier(graph, targetRoot, entry.resource))
                             return new GUIDExclusionFunction(graph);
                     }
index 2203ecaeb6bd792635aa1648495f20c3b5f03956..ec9c8b80c9e8fda57dd623660b6819f7b05e95aa 100644 (file)
@@ -16,44 +16,55 @@ import org.simantics.db.common.request.UniqueRead;
 import org.simantics.db.exception.DatabaseException;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
 import org.simantics.db.layer0.util.DomainProcessor3.ExclusionDecision;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.scl.runtime.function.Function1;
 
 public class TransferableGraphConfiguration2 {
-       
-       public static class RootSpec {
+
+       public static class SeedSpec {
+
+               public static enum SeedSpecType {
+                       INTERNAL, ROOT, SPECIAL_ROOT
+               }
+
                public final Resource resource;
                public final String name;
-               public final boolean internal;
+               // Special roots are not normal seeds - e.g. %model
+               public final SeedSpecType specType;
                /**
                 * Optional, may be null.
                 */
                public final String type;
 
-               public RootSpec(Resource resource, String name, boolean internal) {
-                       this(resource, name, internal, null);
+               public SeedSpec(Resource resource, String name, SeedSpecType specType) {
+                       this(resource, name, specType, null);
                }
 
-               public RootSpec(Resource resource, String name, boolean internal, String type) {
+               public SeedSpec(Resource resource, String name, SeedSpecType specType, String type) {
                        if (resource == null)
                                throw new NullPointerException("null resource");
                        if (name == null)
                                throw new NullPointerException("null name");
                        this.resource = resource;
                        this.name = name;
-                       this.internal = internal;
+                       this.specType = specType;
                        this.type = type;
                }
 
+               public static SeedSpec internal(Resource resource) {
+                       return new SeedSpec(resource, null, SeedSpecType.ROOT);
+               }
+
                @Override
                public String toString() {
-                       return "RootSpec[" + name + ", " + resource + ", " + internal + ", " + type + "]"; 
+                       return "SeedSpec[" + name + ", " + resource + ", " + specType + ", " + type + "]";
                }
 
                @Override
                public int hashCode() {
                        final int prime = 31;
                        int result = 1;
-                       result = prime * result + (internal ? 1231 : 1237);
+                       result = prime * result + specType.hashCode();
                        result = prime * result + resource.hashCode();
                        result = prime * result + name.hashCode();
                        result = prime * result + (type != null ? type.hashCode() : 0);
@@ -68,8 +79,8 @@ public class TransferableGraphConfiguration2 {
                                return false;
                        if (getClass() != obj.getClass())
                                return false;
-                       RootSpec other = (RootSpec) obj;
-                       return internal == other.internal && resource.equals(other.resource) && name.equals(other.name)
+                       SeedSpec other = (SeedSpec) obj;
+                       return specType.equals(other.specType) && resource.equals(other.resource) && name.equals(other.name)
                                        && objectEquals(type, other.type);
                }
 
@@ -81,13 +92,13 @@ public class TransferableGraphConfiguration2 {
                }
        }
 
-       final public TreeMap<String, Variant> baseExtensions = new TreeMap<String,Variant>();
+       final public TreeMap<String, Variant> baseExtensions = new TreeMap<>();
        final public Resource indexRoot;
-       final public Collection<RootSpec> roots;
+       final public Collection<SeedSpec> seeds;
        final public Map<Resource, ExtentStatus> preStatus;
        final public boolean ignoreVirtualResources;
        final public boolean validate;
-       
+
        /**
         * <code>true</code> to export values, <code>false</code> to skip the actual
         * values and only write the resource id.
@@ -97,25 +108,25 @@ public class TransferableGraphConfiguration2 {
        public Collection<TGValueModifier> valueModifiers;
        public Function1<Statement,ExclusionDecision> exclusionFunction;
 
-       public TransferableGraphConfiguration2(Resource indexRoot, Collection<RootSpec> roots, Map<Resource, ExtentStatus> preStatus, boolean ignoreVirtualResources, boolean validate) {
+       public TransferableGraphConfiguration2(Resource indexRoot, Collection<SeedSpec> seeds, Map<Resource, ExtentStatus> preStatus, boolean ignoreVirtualResources, boolean validate) {
                this.indexRoot = indexRoot;
-               this.roots = roots;
+               this.seeds = seeds;
                this.preStatus = preStatus;
                this.ignoreVirtualResources = ignoreVirtualResources;
                this.validate = validate;
                this.valueModifiers = null;
        }
 
-       public TransferableGraphConfiguration2(Resource indexRoot, Collection<RootSpec> roots, Map<Resource, ExtentStatus> preStatus, boolean ignoreVirtualResources) {
+       public TransferableGraphConfiguration2(Resource indexRoot, Collection<SeedSpec> roots, Map<Resource, ExtentStatus> preStatus, boolean ignoreVirtualResources) {
                this(indexRoot, roots, preStatus, ignoreVirtualResources, true);
        }
 
-       public TransferableGraphConfiguration2(Resource indexRoot, Collection<RootSpec> roots, Map<Resource, ExtentStatus> preStatus) {
+       public TransferableGraphConfiguration2(Resource indexRoot, Collection<SeedSpec> roots, Map<Resource, ExtentStatus> preStatus) {
                this(indexRoot, roots, preStatus, true);
        }
 
        public TransferableGraphConfiguration2(TransferableGraphConfiguration2 conf) throws DatabaseException {
-               this(conf.indexRoot, conf.roots, conf.preStatus, conf.ignoreVirtualResources, conf.validate);
+               this(conf.indexRoot, conf.seeds, conf.preStatus, conf.ignoreVirtualResources, conf.validate);
        }
 
        public TransferableGraphConfiguration2(ReadGraph graph, Resource model, boolean ignoreVirtualResources, boolean validate) throws DatabaseException {
@@ -133,12 +144,12 @@ public class TransferableGraphConfiguration2 {
        public TransferableGraphConfiguration2(ReadGraph graph, Resource model) throws DatabaseException {
                this(graph, model, true);
        }
-       
-       public TransferableGraphConfiguration2(ReadGraph graph, Collection<RootSpec> roots, Collection<Resource> resourceRoots, Collection<Resource> exclusions) throws DatabaseException {
+
+       public TransferableGraphConfiguration2(ReadGraph graph, Collection<SeedSpec> roots, Collection<Resource> resourceRoots, Collection<Resource> exclusions) throws DatabaseException {
                this(new TGConfigurer(graph, true).roots(roots).roots2(resourceRoots).exclusions(exclusions).create());
        }
 
-       public TransferableGraphConfiguration2(ReadGraph graph, Collection<RootSpec> roots, Collection<Resource> resourceRoots, Collection<Resource> exclusions, boolean ignoreVirtualResource, boolean validate) throws DatabaseException {
+       public TransferableGraphConfiguration2(ReadGraph graph, Collection<SeedSpec> roots, Collection<Resource> resourceRoots, Collection<Resource> exclusions, boolean ignoreVirtualResource, boolean validate) throws DatabaseException {
                this(new TGConfigurer(graph, ignoreVirtualResource, validate).roots(roots).roots2(resourceRoots).exclusions(exclusions).create());
        }
 
@@ -149,18 +160,18 @@ public class TransferableGraphConfiguration2 {
                        public TransferableGraphConfiguration2 perform(ReadGraph graph) throws DatabaseException {
                                return new TransferableGraphConfiguration2(graph, translate(roots), Collections.<Resource>emptyList(), exclusions, ignoreVirtualResource, validate);
                        }
-                       
+
                });
        }
 
-       public static TransferableGraphConfiguration2 createWithNames2(RequestProcessor processor, final Collection<RootSpec> roots, final Collection<Resource> exclusions, final boolean ignoreVirtualResource, final boolean validate) throws DatabaseException {
+       public static TransferableGraphConfiguration2 createWithNames2(RequestProcessor processor, final Collection<SeedSpec> roots, final Collection<Resource> exclusions, final boolean ignoreVirtualResource, final boolean validate) throws DatabaseException {
                return processor.sync(new UniqueRead<TransferableGraphConfiguration2>() {
 
                        @Override
                        public TransferableGraphConfiguration2 perform(ReadGraph graph) throws DatabaseException {
                                return new TransferableGraphConfiguration2(graph, roots, Collections.<Resource>emptyList(), exclusions, ignoreVirtualResource, validate);
                        }
-                       
+
                });
        }
 
@@ -173,9 +184,9 @@ public class TransferableGraphConfiguration2 {
 
                        @Override
                        public TransferableGraphConfiguration2 perform(ReadGraph graph) throws DatabaseException {
-                               return new TransferableGraphConfiguration2(graph, Collections.<RootSpec>emptyList(), roots, exclusions);
+                               return new TransferableGraphConfiguration2(graph, Collections.<SeedSpec>emptyList(), roots, exclusions);
                        }
-                       
+
                });
        }
 
@@ -183,10 +194,10 @@ public class TransferableGraphConfiguration2 {
                return createWithResources(processor, Collections.singletonList(model), Collections.<Resource>emptyList());
        }
 
-       private static Collection<RootSpec> translate(Collection<NamedResource> roots) {
-               ArrayList<RootSpec> result = new ArrayList<RootSpec>();
-               for(NamedResource nr : roots) result.add(new RootSpec(nr.getResource(), nr.getName(), true));
+       private static Collection<SeedSpec> translate(Collection<NamedResource> roots) {
+               ArrayList<SeedSpec> result = new ArrayList<>();
+               for(NamedResource nr : roots) result.add(new SeedSpec(nr.getResource(), nr.getName(), SeedSpecType.ROOT));
                return result;
        }
-       
+
 }
diff --git a/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest.java b/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest.java
deleted file mode 100644 (file)
index 6b31692..0000000
+++ /dev/null
@@ -1,748 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2007, 2010 Association for Decentralized Information Management
- * in Industry THTH ry.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- *     VTT Technical Research Centre of Finland - initial API and implementation
- *******************************************************************************/
-package org.simantics.db.layer0.util;
-
-import gnu.trove.list.array.TIntArrayList;
-
-import java.io.ByteArrayInputStream;
-import java.io.DataOutput;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.concurrent.ConcurrentSkipListSet;
-import java.util.concurrent.atomic.AtomicInteger;
-
-import org.apache.commons.io.output.DeferredFileOutputStream;
-import org.simantics.databoard.Bindings;
-import org.simantics.databoard.Databoard;
-import org.simantics.databoard.binding.mutable.Variant;
-import org.simantics.databoard.serialization.Serializer;
-import org.simantics.db.AsyncReadGraph;
-import org.simantics.db.ReadGraph;
-import org.simantics.db.Resource;
-import org.simantics.db.Statement;
-import org.simantics.db.common.StandardStatement;
-import org.simantics.db.common.utils.NameUtils;
-import org.simantics.db.exception.DatabaseException;
-import org.simantics.db.exception.ValidationException;
-import org.simantics.db.layer0.adapter.Instances;
-import org.simantics.db.layer0.adapter.SubgraphAdvisor;
-import org.simantics.db.layer0.adapter.SubgraphExtent;
-import org.simantics.db.layer0.adapter.SubgraphExtent.Classifier;
-import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.procedure.AsyncProcedure;
-import org.simantics.db.request.AsyncRead;
-import org.simantics.db.request.Read;
-import org.simantics.db.service.CollectionSupport;
-import org.simantics.db.service.QueryControl;
-import org.simantics.db.service.QueryControl.ControlProcedure;
-import org.simantics.db.service.SerialisationSupport;
-import org.simantics.graph.representation.External;
-import org.simantics.graph.representation.Identity;
-import org.simantics.graph.representation.Root;
-import org.simantics.graph.representation.TransferableGraph1;
-import org.simantics.graph.representation.Value;
-import org.simantics.layer0.Layer0;
-import org.simantics.operation.Layer0X;
-import org.simantics.utils.datastructures.Pair;
-import org.simantics.utils.datastructures.Triple;
-
-/**
- * IsComposedOf objects are always in domain
- * Ordered set elements are always in domain
- * r is in domain if for all statements (s, IsRelatedTo, r) s is in domain
- *
- * IsWeaklyRelatedTo statements where subject is in domain are only accepted if object is in domain or has URI
- * 
- * @deprecated in favor of {@link TransferableGraphRequest2}
- */
-public class TransferableGraphRequest implements Read<TransferableGraph1> {
-
-       public static String LOG_FILE = "transferableGraph.log";
-       final static private boolean LOG = false;
-       final static private boolean DEBUG = false;
-       final static private boolean PROFILE = false;
-       
-//     final private Collection<Pair<Resource, String>> roots;
-//     private Collection<Resource> preExternals = Collections.emptyList();
-//     private Resource model;
-       
-       private TransferableGraphConfiguration configuration;
-       
-       static DataOutput log;
-
-       static {
-
-               if (LOG) {
-                       try {
-                               FileOutputStream stream = new FileOutputStream(LOG_FILE);
-                               log = new DataOutputStream(stream);
-                       } catch (FileNotFoundException e) {
-                               e.printStackTrace();
-                       }
-               }
-
-       }
-       
-       private static void log(String line) {
-               if (LOG) {
-                       try {
-                               log.writeUTF(line + "\n");
-                       } catch (IOException e) {
-                               e.printStackTrace();
-                       }
-               }
-       }
-       
-       
-       
-       public TransferableGraphRequest(Collection<Pair<Resource, String>> roots, Resource model) {
-               
-               configuration = new TransferableGraphConfiguration();
-               configuration.roots = roots;
-               configuration.model = model;
-               
-//             this.roots = roots;
-//             this.model = model;
-               
-       }
-
-       
-       public TransferableGraphRequest(Collection<Pair<Resource, String>> roots) {
-               this(roots, null);
-       }
-
-       public TransferableGraphRequest(TransferableGraphConfiguration conf) {
-               this.configuration = conf;
-       }
-
-       Layer0 l0;
-       
-       TIntArrayList inverses = new TIntArrayList();
-       int statements[];
-       int statementIndex = 0;
-       Map<Resource, Integer> ids;
-       Map<Resource, Variant> values;
-       TIntArrayList externalParents = new TIntArrayList();
-       ArrayList<String> externalNames = new ArrayList<String>(); 
-//     ConcurrentLinkedQueue<Pair<Resource, byte[]>> values = new ConcurrentLinkedQueue<Pair<Resource, byte[]>>();
-       int id = 0;
-       int internalCount;
-       
-       int indent = 0;
-
-       private Serializer variantSerializer;
-
-       private boolean validateExternal(Resource r) {
-               if(configuration.disallowedExternals != null) {
-                       System.err.println("validateExternal agains " + configuration.disallowedExternals);
-                       return !configuration.disallowedExternals.contains(r);
-               }
-               return true;
-       }
-       
-       public int getId(ReadGraph graph, Resource r, Resource predicate) throws DatabaseException {
-//         for(int i=0;i<indent;++i)
-//             System.out.print("  ");
-//         System.out.println(NameUtils.getSafeName(graph, r));
-               if(ids.containsKey(r)) {
-                   int ret = ids.get(r);
-                   if(ret == -1) {
-                       for(int i=0;i<=indent;++i)
-                           System.out.print("  ");
-                       System.out.println("Cycle!!!"); // with " + GraphUtils.getReadableName(g, r));
-                   }
-                       return ret;
-               }
-               else {
-                   //ids.put(r, -1);
-                       Collection<Resource> parents = graph.getObjects(r, l0.PartOf);                  
-                       if(parents.size() != 1) {
-                           if(parents.size() == 0) {
-                               Resource inv = graph.getPossibleObject(r, l0.InverseOf);
-                               if(inv != null) {                       
-                                   ++indent;
-                                   if(DEBUG) System.out.println("inverse " + NameUtils.getSafeName(graph, inv));
-                                   int invId = getId(graph, inv, null);
-                                   externalParents.add(invId);
-                                   --indent;
-                                   externalNames.add("@inverse");
-                                   ids.put(r, id);
-                                   return id++;
-                               }
-                           }
-//                         for(Statement stat : graph.getStatements(r, b.IsWeaklyRelatedTo))
-//                             System.out.println(NameUtils.getSafeName(graph, stat.getPredicate()) 
-//                                 + " -> " + NameUtils.getSafeName(graph, stat.getObject()));
-//                         if(predicate != null) {
-//                             if(!graph.isSubrelationOf(predicate, b.IsRelatedTo)) {
-//                                     return -2;
-//                             }
-//                         }
-                               throw new ValidationException("Reference to external resource " 
-                                               + NameUtils.getSafeName(graph, r, true) + " without unique uri (" + parents.size() + " parents).");
-                       }
-                       for(Resource p : parents) {
-//                 System.out.println("Parent " + NameUtils.getSafeName(graph, p)); 
-                           ++indent;
-                   if(!validateExternal(p)) throw new ValidationException("References to '" + graph.getURI(p) + "' are not allowed.");
-                               externalParents.add(getId(graph, p, null));
-                               --indent;
-                       }
-//          System.out.println("Request named for " + GraphUtils.getReadableName(g, r)); 
-//                     String name = graph.getPossibleRelatedValue(r, b.HasName);
-            externalNames.add((String)graph.getRelatedValue(r, l0.HasName));
-//                     if(name != null) externalNames.add(name);
-//                     else externalNames.add("@resource");
-                       ids.put(r, id);
-                       return id++;
-               }
-       }
-       
-       public void addId(ReadGraph graph, Resource r, Resource predicate) throws DatabaseException {
-               statements[statementIndex++] = getId(graph, r, predicate); 
-       }
-       
-       private void searchStatementPart(ReadGraph graph, final ConcurrentSkipListSet<Statement> statementSet, final ArrayList<Pair<Resource, Triple[]>> part, final Set<SubgraphExtent> extents) throws DatabaseException {
-
-               final SubgraphExtent.Callback callback = new SubgraphExtent.Callback() {
-
-                       @Override
-                       public void statement(Statement statement, boolean accept) {
-                               if(accept) {
-                                       statementSet.add(statement);
-                               }
-                       }
-                       
-               };
-
-               graph.syncRequest(new AsyncRead<Boolean>() {
-
-                   @Override
-                   public int threadHash() {
-                       return hashCode();
-                   }
-                       
-                       @Override
-                       public void perform(AsyncReadGraph graph, AsyncProcedure<Boolean> procedure) {
-
-                               QueryControl control = graph.getService(QueryControl.class);
-
-                               int slice = (int)(part.size() / control.getAmountOfQueryThreads()) + 1;
-
-                               final Pair[] rootArray = (Pair[])part.toArray(new Pair[part.size()]);
-                               for(int i=0;i<control.getAmountOfQueryThreads();i++) {
-
-                                       final int start = i * slice;
-                                       final int end = Math.min(start + slice, rootArray.length);
-
-                                       control.schedule(graph, i, new ControlProcedure() {
-
-                                               @Override
-                                               public void execute(AsyncReadGraph graph) {
-
-                                                       for(int index = start;index < end;index++) {
-
-                                                               final Pair<Resource, Triple[]> r = (Pair<Resource, Triple[]>)rootArray[index];
-
-                                                               final AtomicInteger position = new AtomicInteger(0);
-                                                               final SubgraphExtent.Classifier[] classifiers = new SubgraphExtent.Classifier[extents.size()];
-
-                                                               for(SubgraphExtent extent : extents) {
-
-                                                                       extent.accept(graph, r.first, new AsyncProcedure<Classifier>() {
-
-                                                                               public void execute(AsyncReadGraph graph, Classifier c) {
-
-                                                                                       int current = position.incrementAndGet();
-                                                                                       classifiers[current-1] = c;
-
-                                                                                       if(current == extents.size()) {
-
-                                                                                               for(Triple statement : r.second) {
-                                                                                                       if(!r.first.isPersistent()) continue;
-                                                                                                       for(Classifier classifier : classifiers) {
-                                                                                                               classifier.classify(graph, new StandardStatement(r.first, (Resource)statement.first, (Resource)statement.second), (ExtentStatus)statement.third, callback);
-                                                                                                       }
-                                                                                               }
-                                                                                               
-//                                                                                             graph.forEachDirectStatement(r, new AsyncMultiProcedure<Statement>() {
-//
-//                                                                                                     @Override
-//                                                                                                     public void exception(AsyncReadGraph graph, Throwable throwable) {
-//                                                                                                             throwable.printStackTrace();
-//                                                                                                     }
-//
-//                                                                                                     @Override
-//                                                                                                     public void execute(AsyncReadGraph graph, Statement statement) {
-//                                                                                                     }
-//
-//                                                                                                     @Override
-//                                                                                                     public void finished(AsyncReadGraph graph) {
-//                                                                                                     }
-//
-//                                                                                             });
-
-                                                                                       }
-
-                                                                               }
-
-                                                                               public void exception(AsyncReadGraph graph, Throwable throwable) {
-                                                                                       throwable.printStackTrace();
-                                                                               }
-
-                                                                       }, callback);
-
-                                                               }
-
-                                                       }
-
-                                               }
-
-                                       });
-
-                               }
-
-                               procedure.execute(graph, false);
-
-                       }
-
-                       @Override
-                       public int getFlags() {
-                               return 0;
-                       }
-
-               });
-
-       }
-
-       class StatementSetBuilder {
-
-               private int SLICE = 100000;
-               
-               final private CollectionSupport cs;
-               final private LinkedList<Collection<Statement>> sets = new LinkedList<Collection<Statement>>();
-
-               private Collection<Statement> current;
-               
-               StatementSetBuilder(CollectionSupport cs) {
-                       this.cs = cs;
-                       current = cs.createStatementList();
-               }
-               
-               LinkedList<Collection<Statement>> get() {
-                       sets.add(current);
-                       return sets;
-               }
-               
-               void add(Statement stm) {
-                       current.add(stm);
-                       if(current.size() == SLICE) {
-                               sets.add(current);
-                               current = cs.createStatementList();
-                       }
-               }
-
-               int size() {
-                       int result = 0;
-                       for(Collection<Statement> c : sets) result += c.size();
-                       return result;
-               }
-               
-               
-               void addAll(Collection<Statement> ss) {
-                       for(Statement s : ss) add(s);
-               }
-               
-       }
-       
-       private void searchStatements(ReadGraph graph, ObjectInputStream composedInput, ObjectInputStream statementInput, ObjectInputStream valueInput, final Set<SubgraphExtent> extents) throws DatabaseException, IOException {
-
-               CollectionSupport cs = graph.getService(CollectionSupport.class);
-               
-               ConcurrentSkipListSet<Statement> statementSet = new ConcurrentSkipListSet<Statement>();
-
-               StatementSetBuilder builder = new StatementSetBuilder(cs);
-
-               SerialisationSupport support = graph.getService(SerialisationSupport.class);
-
-               while(composedInput.available() > 0) {
-
-                       int s = composedInput.readInt();
-                       Resource subject = support.getResource(s);
-
-                       int size = composedInput.readInt();
-                       for(int i=0;i<size;i++) {
-                               int p = composedInput.readInt();
-                               int o = composedInput.readInt();
-                               StandardStatement stm = new StandardStatement(subject, support.getResource(p), support.getResource(o));
-//                             if(DEBUG) System.out.println("composed " + NameUtils.toString(graph, stm));
-                               builder.add(stm);
-                       }
-                       
-               }
-
-               while(statementInput.available() > 0) {
-
-                       ArrayList<Pair<Resource, Triple[]>> stms = new ArrayList<Pair<Resource, Triple[]>>(); 
-
-                       int counter = 0;
-                       
-                       while(statementInput.available() > 0 && counter++ < 1000) {
-                       
-                               int s = statementInput.readInt();
-                               Resource subject = support.getResource(s);
-                               int size = statementInput.readInt();
-                               Triple[] list = new Triple[size];
-                               stms.add(Pair.make(subject, list));
-                               for(int i=0;i<size;i++) {
-                                       int p = statementInput.readInt();
-                                       int o = statementInput.readInt();
-                                       if(DEBUG) {
-                                               System.out.println("otherInput " + NameUtils.toString(graph, new StandardStatement(support.getResource(s), support.getResource(p), support.getResource(o))));
-                                       }
-                                       list[i] = new Triple<Resource, Resource, ExtentStatus>(support.getResource(p), support.getResource(o), ExtentStatus.EXTERNAL);
-                               }
-                       }
-                       
-                       searchStatementPart(graph, statementSet, stms, extents);
-                       
-               }
-
-               if(DEBUG) {
-                       for(Statement stm : statementSet)
-                               System.out.println("other " + NameUtils.toString(graph, stm));
-               }
-               
-               builder.addAll(statementSet);
-               
-               if(DEBUG) System.out.println("total " + statementSet.size() + " statements found.");
-
-               statementSet = null;
-               
-               LinkedList<Collection<Statement>> statementSets = builder.get();
-               
-               Map<Resource, Resource> inverses = cs.createMap(Resource.class);
-               Set<Resource> predicateSet = cs.createSet();
-               for(Collection<Statement> set : statementSets)
-                       for(Statement s : set) {
-                               Resource predicate = s.getPredicate();
-                               if(predicateSet.add(predicate)) {
-                                       Resource inverse = graph.getPossibleInverse(predicate);
-                                       inverses.put(predicate, inverse);
-                               }
-                       }
-
-               predicateSet = null;
-               
-               statements = new int[4 * builder.size()];
-               
-        while(!statementSets.isEmpty()) {
-               Collection<Statement> set = statementSets.pop();
-                       for(Statement s : set) {
-                               Resource subject = s.getSubject();
-                               Resource predicate = s.getPredicate();
-                               Resource object = s.getObject();
-                               int subjectId = ids.get(subject);
-                               int objectId = getId(graph, object, predicate);
-                               // The statement can be denied still
-                               if(objectId != -2) {
-                                       statements[statementIndex++] = subjectId;
-                                       addId(graph, predicate, null);
-                                       Resource inverse = inverses.get(predicate);
-                                       if(inverse != null) {
-                                               if(LOG) log("[STM] " + subject.getResourceId() + ", " + predicate.getResourceId() + ", " + inverse.getResourceId() + ", " + object.getResourceId());
-                                               addId(graph, inverse, null);
-                                       } else {
-                                               if(LOG) log("[STM] " + subject.getResourceId() + ", " + predicate.getResourceId() + ", -1, " + object.getResourceId());
-                                               statements[statementIndex++] = -1;
-                                       }
-                                       statements[statementIndex++] = objectId;
-                                       
-                                       
-                                       
-                               } else {
-                                       System.out.println("denied");
-                               }
-                       }
-               }
-               
-               inverses = null;
-               
-               while(valueInput.available() > 0) {
-
-                       int s = valueInput.readInt();
-                       Resource subject = support.getResource(s);
-                       int valueSize = valueInput.readInt();
-                       byte[] value = new byte[valueSize];
-                       valueInput.readFully(value);
-                       Variant variant = (Variant) variantSerializer.deserialize(value);
-                       values.put(subject, variant);
-                       
-               }
-               
-       }
-       
-       public void setExternals(Collection<Resource> rs) {
-               configuration.externals = rs;
-       }
-       
-       @Override
-       public TransferableGraph1 perform(ReadGraph graph) throws DatabaseException {
-
-               this.variantSerializer = graph.getService(Databoard.class).getSerializerUnchecked(Bindings.VARIANT);
-
-               this.l0 = Layer0.getInstance(graph);
-               Layer0X L0X = Layer0X.getInstance(graph);
-               
-               long total = System.nanoTime();
-
-       long startupTime = System.nanoTime();
-
-       CollectionSupport cs = graph.getService(CollectionSupport.class);
-       
-       ids = cs.createMap(Integer.class);
-       values = cs.createMap(byte[].class);
-       
-               ArrayList<Resource> rootResources = new ArrayList<Resource>();
-               for(Pair<Resource, String> p : configuration.roots) rootResources.add(p.first);
-
-//             if(model == null) {
-//                     SimulationResource SIMU = SimulationResource.getInstance(graph);
-//                     for(Resource root : rootResources) {
-//                             if(graph.isInstanceOf(root, SIMU.Model)) {
-//                                     model = root;
-//                                     break;
-//                             }
-//                             model = graph.syncRequest(new TypedParent(root, SIMU.Model));
-//                             if(model != null) break;
-//                     }
-//             }
-
-               Map<Resource, ExtentStatus> preStatus = new HashMap<Resource, ExtentStatus>();
-               
-               for(Resource root : rootResources) {
-                       Resource name = graph.getPossibleObject(root, l0.HasName);
-                       if(name != null) {
-                               preStatus.put(name, ExtentStatus.EXCLUDED);
-                       }
-               }
-               
-               for(Resource r : configuration.externals) preStatus.put(r, ExtentStatus.EXTERNAL); 
-
-               Set<SubgraphExtent> extents = configuration.extents;
-               if(extents == null) {
-                       
-                       Instances extentInstances = graph.adapt(L0X.SubgraphExtent, Instances.class);
-                       Collection<Resource> extentResources = extentInstances.find(graph, configuration.model);
-                       extents = new HashSet<SubgraphExtent>();
-                       for(Resource r : extentResources) {
-                               extents.add(graph.getPossibleAdapter(r, SubgraphExtent.class));
-                       }
-
-                       if(DEBUG) {
-                               System.out.println("Extents " + extents.size());
-                               for(Resource extent : extentResources) System.out.println("-" + NameUtils.getSafeName(graph, extent));
-                       }
-                       
-               }
-               
-               Set<SubgraphAdvisor> advisors = configuration.advisors;
-               if(advisors == null) {
-
-                       Instances advisorInstances = graph.adapt(L0X.SubgraphAdvisor, Instances.class);
-                       Collection<Resource> advisorResources = advisorInstances.find(graph, configuration.model);
-                       advisors = new HashSet<SubgraphAdvisor>();
-                       for(Resource r : advisorResources) {
-                               advisors.add(graph.getPossibleAdapter(r, SubgraphAdvisor.class));
-                       }
-
-                       if(DEBUG) {
-                               System.out.println("Advisors " + advisors.size());
-                               for(Resource advisor : advisorResources) System.out.println("-" + NameUtils.getSafeName(graph, advisor));
-                       }
-                       
-               }
-
-       long startupTimeEnd = System.nanoTime();
-
-               long domainTime = System.nanoTime();
-               
-               String composedStatements = "composed" + UUID.randomUUID().toString();
-               String otherStatements = "other" + UUID.randomUUID().toString();
-               String valueFileName = "value" + UUID.randomUUID().toString();
-               
-        File composedStatementsFile = new File(composedStatements);
-        File otherStatementsFile = new File(otherStatements);
-        File valueFile = new File(valueFileName);
-        
-        if(DEBUG)
-               System.out.println("getDomain writes " + composedStatementsFile.getAbsolutePath());
-
-        try {
-        
-               DeferredFileOutputStream composedStatementsStream = new DeferredFileOutputStream(5 * 1024*1024, composedStatementsFile);
-               DeferredFileOutputStream otherStatementsStream = new DeferredFileOutputStream(1024*1024, otherStatementsFile);
-               DeferredFileOutputStream valueStream = new DeferredFileOutputStream(1024*1024, valueFile);
-               
-               ObjectOutputStream composedStatementsOutput = new ObjectOutputStream(composedStatementsStream);
-               ObjectOutputStream otherStatementsOutput = new ObjectOutputStream(otherStatementsStream);
-               ObjectOutputStream valueOutput = new ObjectOutputStream(valueStream);
-
-               Subgraphs.getDomain(graph, ids, rootResources, preStatus, advisors, composedStatementsOutput, otherStatementsOutput, valueOutput);
-               id = ids.size();
-
-               composedStatementsOutput.flush();
-               otherStatementsOutput.flush();
-               valueOutput.flush();
-               composedStatementsStream.close();
-               otherStatementsStream.close();
-               valueStream.close();
-               
-               long domainTimeEnd = System.nanoTime();
-
-               long fileTime = System.nanoTime();
-
-               internalCount = id;
-
-               ids.put(graph.getRootLibrary(), id++);
-               externalNames.add("http:/");
-               externalParents.add(-1);
-
-//             if(model == null) return null;
-
-               InputStream composedStatementsInputStream = null;
-               InputStream otherStatementsInputStream = null;
-               InputStream valueInputStream = null;
-               
-               if(composedStatementsStream.isInMemory()) {
-                       composedStatementsInputStream = new ByteArrayInputStream(composedStatementsStream.getData());
-               } else {
-                       composedStatementsInputStream = new FileInputStream(composedStatementsFile);
-               }
-               
-               if(otherStatementsStream.isInMemory()) {
-                       otherStatementsInputStream = new ByteArrayInputStream(otherStatementsStream.getData());
-               } else {
-                       otherStatementsInputStream = new FileInputStream(otherStatementsFile);
-               }
-
-               if(valueStream.isInMemory()) {
-                       valueInputStream = new ByteArrayInputStream(valueStream.getData());
-               } else {
-                       valueInputStream = new FileInputStream(valueFile);
-               }
-
-               composedStatementsStream = null;
-               otherStatementsStream = null;
-               valueStream = null;
-               
-               ObjectInputStream composedStatementsInput = new ObjectInputStream(composedStatementsInputStream);
-               ObjectInputStream otherStatementsInput = new ObjectInputStream(otherStatementsInputStream);
-               ObjectInputStream valueInput = new ObjectInputStream(valueInputStream);
-
-               long fileTimeEnd = System.nanoTime();
-
-               long statementTime = System.nanoTime();
-               searchStatements(graph, composedStatementsInput, otherStatementsInput, valueInput, extents);
-               long statementTimeEnd = System.nanoTime();
-
-               //              domainParts = null;
-
-               long buildTime = System.nanoTime();
-
-               int resourceCount = ids.size();
-
-               Identity[] identityArray;
-               { // Identities
-                       ArrayList<Identity> identities = new ArrayList<Identity>();
-
-                       for(Pair<Resource, String> r : configuration.roots) {
-                               Resource type = graph.getPossibleType(r.first, l0.Entity);
-                               if(type == null) type = l0.Entity;
-                               identities.add(new Identity(
-                                               ids.get(r.first),
-                                               new Root(r.second, graph.getURI(type))
-                               ));
-                       }
-
-                       int internalsPlusExternals = ids.size();                
-                       for(int i = internalCount; i < internalsPlusExternals ; i++) {
-                               int parent = externalParents.get(i - internalCount);
-                               String name = externalNames.get(i - internalCount);
-                               identities.add(new Identity(
-                                               i, 
-                                               new External(parent, name)
-                               ));
-                       }
-                       identityArray = identities.toArray(new Identity[identities.size()]);
-               }            
-
-               Value[] valueArray = new Value[values.size()];
-               { // Values
-                       int index = 0;
-                       for(Map.Entry<Resource, Variant> entry : values.entrySet()) {
-                               if(LOG) log("[VALUE] " + entry.getKey().getResourceId());
-                               int r = getId(graph, entry.getKey(), null);
-                               valueArray[index++] = new Value(r, entry.getValue());
-                       }
-               }
-               ids = null;
-               values = null;
-
-               long buildTimeEnd = System.nanoTime();
-
-               TransferableGraph1 result = 
-                   new TransferableGraph1(resourceCount, 
-                           identityArray, 
-                           statements, 
-                           valueArray);
-
-               if(DEBUG) {
-                       System.out.println("transferable graph content: " + result);
-               }
-
-               long totalEnd = System.nanoTime();
-
-               if(PROFILE) {   
-                       System.out.println("startup in " + 1e-9*(startupTimeEnd - startupTime) + "s.");
-                       System.out.println("domain was found in " + 1e-9*(domainTimeEnd - domainTime) + "s.");
-                       System.out.println("files were written in " + 1e-9*(fileTimeEnd - fileTime) + "s.");
-                       System.out.println("statements were found in " + 1e-9*(statementTimeEnd - statementTime) + "s.");
-                       System.out.println("tg was built in " + 1e-9*(buildTimeEnd - buildTime) + "s.");
-                       System.out.println("total time for building subgraph was " + 1e-9*(totalEnd-total) + "s.");
-               }               
-
-               return result;
-        } catch (IOException e) {
-               e.printStackTrace();
-        }
-               
-        return null;
-               
-       }
-       
-}
diff --git a/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest2.java b/bundles/org.simantics.db.layer0/src/org/simantics/db/layer0/util/TransferableGraphRequest2.java
deleted file mode 100644 (file)
index c95a565..0000000
+++ /dev/null
@@ -1,509 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2007, 2010 Association for Decentralized Information Management
- * in Industry THTH ry.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- *     VTT Technical Research Centre of Finland - initial API and implementation
- *******************************************************************************/
-package org.simantics.db.layer0.util;
-
-import gnu.trove.list.array.TIntArrayList;
-import gnu.trove.map.TIntObjectMap;
-import gnu.trove.map.hash.TIntIntHashMap;
-import gnu.trove.map.hash.TIntObjectHashMap;
-import gnu.trove.procedure.TIntObjectProcedure;
-import gnu.trove.set.hash.TIntHashSet;
-
-import java.io.ByteArrayInputStream;
-import java.io.DataOutput;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.lang.management.ManagementFactory;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.UUID;
-
-import org.apache.commons.io.output.DeferredFileOutputStream;
-import org.simantics.databoard.Bindings;
-import org.simantics.databoard.binding.mutable.Variant;
-import org.simantics.db.ReadGraph;
-import org.simantics.db.Resource;
-import org.simantics.db.common.utils.NameUtils;
-import org.simantics.db.exception.DatabaseException;
-import org.simantics.db.exception.ValidationException;
-import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
-import org.simantics.db.request.Read;
-import org.simantics.db.service.ClusterControl;
-import org.simantics.db.service.ClusterControl.ClusterState;
-import org.simantics.db.service.SerialisationSupport;
-import org.simantics.graph.representation.External;
-import org.simantics.graph.representation.Identity;
-import org.simantics.graph.representation.Root;
-import org.simantics.graph.representation.TransferableGraph1;
-import org.simantics.graph.representation.Value;
-import org.simantics.layer0.Layer0;
-import org.simantics.utils.datastructures.Pair;
-
-/**
- * @deprecated in favor of {@link ModelTransferableGraphSourceRequest}
- */
-@Deprecated
-public class TransferableGraphRequest2 implements Read<TransferableGraph1> {
-
-       public static String LOG_FILE = "transferableGraph.log";
-       final static private boolean LOG = false;
-       final static private boolean DEBUG = false;
-       final static private boolean PROFILE = false;
-       
-       private TransferableGraphConfiguration configuration;
-       
-       static DataOutput log;
-
-       static {
-
-               if (LOG) {
-                       try {
-                               FileOutputStream stream = new FileOutputStream(LOG_FILE);
-                               log = new DataOutputStream(stream);
-                       } catch (FileNotFoundException e) {
-                               e.printStackTrace();
-                       }
-               }
-
-       }
-       
-       private static void log(String line) {
-               if (LOG) {
-                       try {
-                               log.writeUTF(line + "\n");
-                       } catch (IOException e) {
-                               e.printStackTrace();
-                       }
-               }
-       }
-       
-       
-       
-       public TransferableGraphRequest2(Collection<Pair<Resource, String>> roots, Resource model) {
-               
-               configuration = new TransferableGraphConfiguration();
-               configuration.roots = roots;
-               configuration.model = model;
-               
-       }
-
-       
-       public TransferableGraphRequest2(Collection<Pair<Resource, String>> roots) {
-               this(roots, null);
-       }
-
-       public TransferableGraphRequest2(TransferableGraphConfiguration conf) {
-               this.configuration = conf;
-       }
-
-       Layer0 L0;
-       
-       TIntArrayList inverses = new TIntArrayList();
-       int statements[];
-       int statementIndex = 0;
-       TIntIntHashMap ids;
-       TIntObjectMap<Variant> values;
-       TIntArrayList externalParents = new TIntArrayList();
-       ArrayList<String> externalNames = new ArrayList<String>(); 
-       int id = 0;
-       int internalCount;
-       
-       int indent = 0;
-
-       private SerialisationSupport support;
-
-       private boolean validateExternal(Resource r) {
-               if(configuration.disallowedExternals != null) {
-                       System.err.println("validateExternal agains " + configuration.disallowedExternals);
-                       return !configuration.disallowedExternals.contains(r);
-               }
-               return true;
-       }
-       
-       private Resource getResource(int r) throws DatabaseException {
-               return support.getResource(r);
-       }
-       
-       public int getInternalId(int r) {
-               return ids.get(r);
-       }
-       
-       public int getId(ReadGraph graph, int r, int predicate) throws DatabaseException {
-               if(ids.containsKey(r)) {
-                   int ret = ids.get(r);
-                   if(ret == -1) {
-                       for(int i=0;i<=indent;++i)
-                           System.out.print("  ");
-                       System.out.println("Cycle!!!"); // with " + GraphUtils.getReadableName(g, r));
-                   }
-                       return ret;
-               }
-               else {
-                       Collection<Resource> parents = graph.getObjects(getResource(r), L0.PartOf);                     
-                       if(parents.size() != 1) {
-                               throw new ValidationException("Reference to external resource " 
-                                               + NameUtils.getSafeName(graph, getResource(r), true) + " without unique uri (" + parents.size() + " parents).");
-                       }
-                       for(Resource p : parents) {
-                           ++indent;
-                   if(!validateExternal(p)) throw new ValidationException("References to '" + graph.getURI(p) + "' are not allowed.");
-                               externalParents.add(getId(graph, support.getTransientId(p), 0));
-                               --indent;
-                       }
-            externalNames.add((String)graph.getRelatedValue(getResource(r), L0.HasName));
-                       ids.put(r, id);
-                       return id++;
-               }
-       }
-       
-       public void addId(ReadGraph graph, int r, int predicate) throws DatabaseException {
-               statements[statementIndex++] = getId(graph, r, predicate); 
-       }
-       
-       public void setExternals(Collection<Resource> rs) {
-               configuration.externals = rs;
-       }
-       
-       @Override
-       public TransferableGraph1 perform(ReadGraph graph) throws DatabaseException {
-
-               support = graph.getService(SerialisationSupport.class);
-
-               this.L0 = Layer0.getInstance(graph);    
-
-               long total = System.nanoTime();
-
-       long startupTime = System.nanoTime();
-
-       ClusterControl cc = graph.getService(ClusterControl.class);
-       
-       ids = new TIntIntHashMap();
-       values = new TIntObjectHashMap<Variant>();
-       
-               ArrayList<Resource> rootResources = new ArrayList<Resource>();
-               for(Pair<Resource, String> p : configuration.roots) rootResources.add(p.first);
-
-               Map<Resource, ExtentStatus> preStatus = new HashMap<Resource, ExtentStatus>();
-               
-               for(Resource root : rootResources) {
-                       Resource name = graph.getPossibleObject(root, L0.HasName);
-                       if(name != null) {
-                               preStatus.put(name, ExtentStatus.EXCLUDED);
-                       }
-               }
-               
-               for(Resource r : configuration.externals) preStatus.put(r, ExtentStatus.EXTERNAL); 
-
-       long startupTimeEnd = System.nanoTime();
-
-               long domainTime = System.nanoTime();
-               
-               String otherStatements = "other" + UUID.randomUUID().toString();
-               String valueFileName = "value" + UUID.randomUUID().toString();
-               
-        File otherStatementsFile = new File(otherStatements);
-        File valueFile = new File(valueFileName);
-        
-        try {
-        
-               DeferredFileOutputStream otherStatementsStream = new DeferredFileOutputStream(1024*1024, otherStatementsFile);
-               DeferredFileOutputStream valueStream = new DeferredFileOutputStream(1024*1024, valueFile);
-               
-               ObjectOutputStream otherStatementsOutput = new ObjectOutputStream(otherStatementsStream);
-               ObjectOutputStream valueOutput = new ObjectOutputStream(valueStream);
-
-               ClusterState clusterState = cc.getClusterState();
-
-               TIntHashSet excludedShared = new TIntHashSet();
-               
-               TreeMap<String, Variant> extensions = new TreeMap<String, Variant>();
-               
-               Subgraphs.getDomain2(graph, ids, rootResources, preStatus, configuration.specials, otherStatementsOutput, valueOutput, extensions, excludedShared);
-               
-               id = ids.size();
-
-               cc.restoreClusterState(clusterState);
-
-//             dumpHeap("domain.hprof");
-
-               otherStatementsOutput.flush();
-               valueOutput.flush();
-               otherStatementsStream.close();
-               valueStream.close();
-               
-               long domainDuration = System.nanoTime() - domainTime;
-               System.err.println("Analysed graph in " + 1e-9*domainDuration + "s.");
-
-               internalCount = id;
-
-               ids.put(support.getTransientId(graph.getResource("http:/")), id++);
-               externalNames.add("http:/");
-               externalParents.add(-1);
-
-               InputStream otherStatementsInputStream = null;
-               InputStream valueInputStream = null;
-               
-               if(otherStatementsStream.isInMemory()) {
-                       otherStatementsInputStream = new ByteArrayInputStream(otherStatementsStream.getData());
-               } else {
-                       otherStatementsInputStream = new FileInputStream(otherStatementsFile);
-               }
-
-               if(valueStream.isInMemory()) {
-                       valueInputStream = new ByteArrayInputStream(valueStream.getData());
-               } else {
-                       valueInputStream = new FileInputStream(valueFile);
-               }
-
-               otherStatementsStream = null;
-               valueStream = null;
-               
-               ObjectInputStream otherStatementsInput = new ObjectInputStream(otherStatementsInputStream);
-               ObjectInputStream valueInput = new ObjectInputStream(valueInputStream);
-
-               long statementTime = System.nanoTime();
-               
-               TIntArrayList statementSet = new TIntArrayList();
-               
-               while(otherStatementsInput.available() > 0) {
-                       
-                       int s = otherStatementsInput.readInt();
-                       
-                       boolean exclude = !ids.contains(s);
-                       
-                       int size = otherStatementsInput.readInt();
-                       for(int i=0;i<size;i++) {
-                               int p = otherStatementsInput.readInt();
-                               int o = otherStatementsInput.readInt();
-                               if(!exclude) {
-                                       if(excludedShared.contains(o)) {
-//                                             System.err.println("excluding shared " + s + " " + p + " " + o);
-                                       } else {
-                                               statementSet.add(s);
-                                               statementSet.add(p);
-                                               statementSet.add(o);
-                                       }
-                               } else {
-//                                             System.err.println("excluding shared " + s);
-                               }
-                       }
-                       
-               }
-
-               TIntIntHashMap inverses = new TIntIntHashMap();
-               TIntHashSet predicateSet = new TIntHashSet();
-               for(int i=0;i<statementSet.size();i+=3) {
-                       int p = statementSet.getQuick(i+1);
-                       if(predicateSet.add(p)) {
-                                       Resource inverse = graph.getPossibleInverse(getResource(p));
-                                       if(inverse != null) inverses.put(p, support.getTransientId(inverse));
-                       }
-               }
-                       
-               predicateSet = null;
-               
-               TIntArrayList tgStatements = new TIntArrayList();
-               
-//             dumpHeap("export.hprof");
-
-               // 25%
-               int trim = Math.max(65536,statementSet.size()/12);
-               
-               for(int i=statementSet.size();i>0;i-=3) {
-
-                       if(trim-- == 0) {
-                               statementSet.remove(i, statementSet.size()-i);
-                               statementSet.trimToSize();
-                               trim = Math.max(65536,statementSet.size()/12);
-                       }
-
-                       int s = statementSet.getQuick(i-3);
-                       int p = statementSet.getQuick(i-2);
-                       int o = statementSet.getQuick(i-1);
-               
-                       int subjectId = ids.get(s);
-                       if(subjectId >= internalCount) System.err.println("Statement for external: " + s + " " + p + " " + o);
-                       
-                       int objectId = getId(graph, o, p);
-                       // The statement can be denied still
-                       if(objectId != -2) {
-                               tgStatements.add(subjectId);
-                               tgStatements.add(getId(graph, p, 0));
-                               int inverse = inverses.get(p);
-                               if(inverse != 0) {
-                                       tgStatements.add(getId(graph, inverse, 0));
-                               } else {
-                                       tgStatements.add(-1);
-                               }
-                               tgStatements.add(objectId);
-                       } else {
-                               System.out.println("denied");
-                       }
-                       
-               }
-               
-               statements = tgStatements.toArray();
-
-               long statementDuration = System.nanoTime() - statementTime;
-               System.err.println("Built transferable statements in " + 1e-9*statementDuration + "s.");
-               
-               inverses = null;
-               
-               while(valueInput.available() > 0) {
-
-                       int s = valueInput.readInt();
-//                     Resource subject = support.getResource(s);
-                       int valueSize = valueInput.readInt();
-                       byte[] value = new byte[valueSize];
-                       valueInput.readFully(value);
-                       Variant variant = (Variant)Bindings.VARIANT.serializer().deserialize(value);
-                       values.put(s, variant);
-                       
-               }
-
-               int resourceCount = ids.size();
-
-               Identity[] identityArray;
-               { // Identities
-                       ArrayList<Identity> identities = new ArrayList<Identity>();
-
-                       for(Pair<Resource, String> r : configuration.roots) {
-                               Resource type = graph.getPossibleType(r.first, L0.Entity);
-                               if(type == null) type = L0.Entity;
-                               identities.add(new Identity(
-                                               ids.get(support.getTransientId(r.first)),
-                                               new Root(r.second, graph.getURI(type))
-                               ));
-                       }
-
-                       int internalsPlusExternals = ids.size();                
-                       for(int i = internalCount; i < internalsPlusExternals ; i++) {
-                               int parent = externalParents.get(i - internalCount);
-                               String name = externalNames.get(i - internalCount);
-                               identities.add(new Identity(
-                                               i, 
-                                               new External(parent, name)
-                               ));
-                       }
-                       identityArray = identities.toArray(new Identity[identities.size()]);
-               }       
-            
-            final Value[] valueArray = new Value[values.size()];
-               { // Values
-                       values.forEachEntry(new TIntObjectProcedure<Variant>() {
-
-                       int index = 0;
-
-                                       @Override
-                                       public boolean execute(int subject, Variant bytes) {
-                                       //if(LOG) log("[VALUE] " + entry.getKey().getResourceId());
-                                       int r = getInternalId(subject);
-                                       if(r==-1) System.err.println("No id for value resource " + subject);
-                                       else valueArray[index++] = new Value(r, bytes);
-                                       return true;
-                                       }
-                                       
-                               });
-               }
-            ids = null;
-               values = null;
-
-            TransferableGraph1 result = 
-                new TransferableGraph1(resourceCount, 
-                        identityArray, 
-                        statements, 
-                        valueArray, extensions);
-            
-               if(DEBUG) {
-                       System.out.println("transferable graph content: " + result);
-               }
-
-               long totalEnd = System.nanoTime();
-
-               if(PROFILE) {   
-                       System.out.println("startup in " + 1e-9*(startupTimeEnd - startupTime) + "s.");
-                       System.out.println("domain was found in " + 1e-9*(domainDuration) + "s.");
-                       System.out.println("statements were found in " + 1e-9*(statementDuration) + "s.");
-                       System.out.println("total time for building subgraph was " + 1e-9*(totalEnd-total) + "s.");
-               }
-
-               return result;
-
-        } catch (IOException e) {
-               e.printStackTrace();
-        } catch (Throwable t) {
-               t.printStackTrace();
-               dumpHeap("crash.hprof");
-        }
-               
-        return null;
-               
-       }
-
-       private static void dumpHeap(String path) {
-               
-        try {
-            Object bean = getBean();
-            if (bean == null)
-                return;
-
-            Method m = bean.getClass().getMethod("dumpHeap", String.class, boolean.class);
-            m.invoke(bean, path, true);
-            
-        } catch (IllegalArgumentException e) {
-        } catch (IllegalAccessException e) {
-        } catch (SecurityException e) {
-        } catch (NoSuchMethodException e) {
-        } catch (InvocationTargetException e) {
-               } finally {
-        }
-               
-       }
-       
-    private static Object getBean() {
-        Class<?> beanClass = getBeanClass();
-        if (beanClass == null)
-            return null;
-        try {
-            Object bean = ManagementFactory.newPlatformMXBeanProxy(
-                    ManagementFactory.getPlatformMBeanServer(),
-                    "com.sun.management:type=HotSpotDiagnostic",
-                    beanClass);
-            return bean;
-        } catch (IOException e) {
-            return null;
-        }
-    }
-    
-    private static Class<?> getBeanClass() {
-        try {
-            Class<?> clazz = Class.forName("com.sun.management.HotSpotDiagnosticMXBean");
-            return clazz;
-        } catch (ClassNotFoundException e) {
-            return null;
-        }
-    }
-    
-       
-}
index 5472ccfd61918ee6fb5932e75eaec6a349138bde..c9b48b32591fce602c7a5aacec56c23f3b7fe9c9 100644 (file)
@@ -251,11 +251,13 @@ public class StreamingTransferableGraphImportProcess implements TransferableGrap
 
        @Override
        public Resource createChild(WriteOnlyGraph graph, Resource parent, Resource child, String name) throws DatabaseException {
+               //System.err.println("child " + parent + " - " + child + " = " + name);
            if(child == null) child = graph.newResource();
                Resource nameResource = graph.newResource();
                graph.claim(nameResource, InstanceOf, null, String);
                graph.claimValue(nameResource, name, WriteBindings.STRING);
                graph.claim(child, HasName, NameOf, nameResource);
+               graph.claim(parent,  ConsistsOf, PartOf, child);
                return child;
        }
 
@@ -457,7 +459,6 @@ public class StreamingTransferableGraphImportProcess implements TransferableGrap
                        }
                        else if(definition instanceof Internal) {
                                Internal def = (Internal)definition;
-                               
                                Resource external = existingInternalMap.get(identity.resource);
                                if(external != null) {
                                        handles[identity.resource] = builder.handle(external);
index 6167334fdd79815ad98a60cb1db1762d611a116f..8c91852cdd83b143189290654b0fa814f4b7fa79 100644 (file)
@@ -26,7 +26,8 @@ import org.simantics.db.function.DbConsumer;
 import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;
 import org.simantics.db.layer0.adapter.impl.DefaultCopyHandler;
 import org.simantics.db.layer0.util.TransferableGraphConfiguration2;
-import org.simantics.db.layer0.util.TransferableGraphConfiguration2.RootSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec;
+import org.simantics.db.layer0.util.TransferableGraphConfiguration2.SeedSpec.SeedSpecType;
 import org.simantics.diagram.stubs.DiagramResource;
 import org.simantics.layer0.Layer0;
 import org.simantics.modeling.ModelingResources;
@@ -59,7 +60,7 @@ public class CompositeCopyHandler extends DefaultCopyHandler {
                 ? (Set<Resource>) resources : new HashSet<>(resources);
         Set<Resource> exclusions = new HashSet<>();
         Set<Resource> externals = new HashSet<>();
-        List<RootSpec> roots = new ArrayList<>();
+        List<SeedSpec> roots = new ArrayList<>();
 
         Resource indexRoot = graph.syncRequest(new PossibleIndexRoot(resources.iterator().next()));
         if(indexRoot == null) throw new DatabaseException("Composite is not part of any index root");
@@ -143,17 +144,17 @@ public class CompositeCopyHandler extends DefaultCopyHandler {
 
             // Include resource as root
             CompositeInfo info = CompositeInfo.fromResource(graph, resource);
-            roots.add(new RootSpec(resource, info.getTGName(), true, typeId(graph, L0, indexRootUri, resource)));
+            roots.add(new SeedSpec(resource, info.getTGName(), SeedSpecType.ROOT, typeId(graph, L0, indexRootUri, resource)));
             identifierExcluder.accept(resource);
             // Include components as roots
             for (Resource child : graph.sync(new ObjectsWithType(resource, L0.ConsistsOf, SR.Component))) {
                 DiagramComponentInfo cinfo = DiagramComponentInfo.fromResource(graph, info, child);
                 identifierExcluder.accept(child);
-                roots.add(new RootSpec(child, cinfo.getTGName(info), true, typeId(graph, L0, indexRootUri, child)));
+                roots.add(new SeedSpec(child, cinfo.getTGName(info), SeedSpecType.ROOT, typeId(graph, L0, indexRootUri, child)));
             }
         }
 
-        roots.add(new RootSpec(indexRoot, "%model", false));
+        roots.add(new SeedSpec(indexRoot, "%model", SeedSpecType.SPECIAL_ROOT));
 
         TransferableGraphConfiguration2 config = TransferableGraphConfiguration2.createWithNames2(graph, roots, exclusions, true, false);
         for (Resource external : externals)