--- /dev/null
+/*******************************************************************************\r
+ * Copyright (c) 2007, 2010 Association for Decentralized Information Management\r
+ * in Industry THTH ry.\r
+ * All rights reserved. This program and the accompanying materials\r
+ * are made available under the terms of the Eclipse Public License v1.0\r
+ * which accompanies this distribution, and is available at\r
+ * http://www.eclipse.org/legal/epl-v10.html\r
+ *\r
+ * Contributors:\r
+ * VTT Technical Research Centre of Finland - initial API and implementation\r
+ *******************************************************************************/\r
+package org.simantics.db.layer0.util;\r
+\r
+import gnu.trove.list.array.TIntArrayList;\r
+import gnu.trove.map.TIntObjectMap;\r
+import gnu.trove.map.hash.TIntIntHashMap;\r
+import gnu.trove.map.hash.TIntObjectHashMap;\r
+import gnu.trove.procedure.TIntObjectProcedure;\r
+import gnu.trove.set.hash.TIntHashSet;\r
+\r
+import java.io.ByteArrayInputStream;\r
+import java.io.DataOutput;\r
+import java.io.DataOutputStream;\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileOutputStream;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.io.ObjectInputStream;\r
+import java.io.ObjectOutputStream;\r
+import java.lang.management.ManagementFactory;\r
+import java.lang.reflect.InvocationTargetException;\r
+import java.lang.reflect.Method;\r
+import java.util.ArrayList;\r
+import java.util.Collection;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+import java.util.TreeMap;\r
+import java.util.UUID;\r
+\r
+import org.apache.commons.io.output.DeferredFileOutputStream;\r
+import org.simantics.databoard.Bindings;\r
+import org.simantics.databoard.binding.mutable.Variant;\r
+import org.simantics.db.ReadGraph;\r
+import org.simantics.db.Resource;\r
+import org.simantics.db.common.utils.NameUtils;\r
+import org.simantics.db.exception.DatabaseException;\r
+import org.simantics.db.exception.ValidationException;\r
+import org.simantics.db.layer0.adapter.SubgraphExtent.ExtentStatus;\r
+import org.simantics.db.request.Read;\r
+import org.simantics.db.service.ClusterControl;\r
+import org.simantics.db.service.ClusterControl.ClusterState;\r
+import org.simantics.db.service.SerialisationSupport;\r
+import org.simantics.graph.representation.External;\r
+import org.simantics.graph.representation.Identity;\r
+import org.simantics.graph.representation.Root;\r
+import org.simantics.graph.representation.TransferableGraph1;\r
+import org.simantics.graph.representation.Value;\r
+import org.simantics.layer0.Layer0;\r
+import org.simantics.utils.datastructures.Pair;\r
+\r
+public class TransferableGraphRequest2 implements Read<TransferableGraph1> {\r
+\r
+ public static String LOG_FILE = "transferableGraph.log";\r
+ final static private boolean LOG = false;\r
+ final static private boolean DEBUG = false;\r
+ final static private boolean PROFILE = false;\r
+ \r
+ private TransferableGraphConfiguration configuration;\r
+ \r
+ static DataOutput log;\r
+\r
+ static {\r
+\r
+ if (LOG) {\r
+ try {\r
+ FileOutputStream stream = new FileOutputStream(LOG_FILE);\r
+ log = new DataOutputStream(stream);\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+\r
+ }\r
+ \r
+ private static void log(String line) {\r
+ if (LOG) {\r
+ try {\r
+ log.writeUTF(line + "\n");\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ \r
+ \r
+ \r
+ public TransferableGraphRequest2(Collection<Pair<Resource, String>> roots, Resource model) {\r
+ \r
+ configuration = new TransferableGraphConfiguration();\r
+ configuration.roots = roots;\r
+ configuration.model = model;\r
+ \r
+ }\r
+\r
+ \r
+ public TransferableGraphRequest2(Collection<Pair<Resource, String>> roots) {\r
+ this(roots, null);\r
+ }\r
+\r
+ public TransferableGraphRequest2(TransferableGraphConfiguration conf) {\r
+ this.configuration = conf;\r
+ }\r
+\r
+ Layer0 L0;\r
+ \r
+ TIntArrayList inverses = new TIntArrayList();\r
+ int statements[];\r
+ int statementIndex = 0;\r
+ TIntIntHashMap ids;\r
+ TIntObjectMap<Variant> values;\r
+ TIntArrayList externalParents = new TIntArrayList();\r
+ ArrayList<String> externalNames = new ArrayList<String>(); \r
+ int id = 0;\r
+ int internalCount;\r
+ \r
+ int indent = 0;\r
+\r
+ private SerialisationSupport support;\r
+\r
+ private boolean validateExternal(Resource r) {\r
+ if(configuration.disallowedExternals != null) {\r
+ System.err.println("validateExternal agains " + configuration.disallowedExternals);\r
+ return !configuration.disallowedExternals.contains(r);\r
+ }\r
+ return true;\r
+ }\r
+ \r
+ private Resource getResource(int r) throws DatabaseException {\r
+ return support.getResource(r);\r
+ }\r
+ \r
+ public int getInternalId(int r) {\r
+ return ids.get(r);\r
+ }\r
+ \r
+ public int getId(ReadGraph graph, int r, int predicate) throws DatabaseException {\r
+ if(ids.containsKey(r)) {\r
+ int ret = ids.get(r);\r
+ if(ret == -1) {\r
+ for(int i=0;i<=indent;++i)\r
+ System.out.print(" ");\r
+ System.out.println("Cycle!!!"); // with " + GraphUtils.getReadableName(g, r));\r
+ }\r
+ return ret;\r
+ }\r
+ else {\r
+ Collection<Resource> parents = graph.getObjects(getResource(r), L0.PartOf); \r
+ if(parents.size() != 1) {\r
+ throw new ValidationException("Reference to external resource " \r
+ + NameUtils.getSafeName(graph, getResource(r), true) + " without unique uri (" + parents.size() + " parents).");\r
+ }\r
+ for(Resource p : parents) {\r
+ ++indent;\r
+ if(!validateExternal(p)) throw new ValidationException("References to '" + graph.getURI(p) + "' are not allowed.");\r
+ externalParents.add(getId(graph, support.getTransientId(p), 0));\r
+ --indent;\r
+ }\r
+ externalNames.add((String)graph.getRelatedValue(getResource(r), L0.HasName));\r
+ ids.put(r, id);\r
+ return id++;\r
+ }\r
+ }\r
+ \r
+ public void addId(ReadGraph graph, int r, int predicate) throws DatabaseException {\r
+ statements[statementIndex++] = getId(graph, r, predicate); \r
+ }\r
+ \r
+ public void setExternals(Collection<Resource> rs) {\r
+ configuration.externals = rs;\r
+ }\r
+ \r
+ @Override\r
+ public TransferableGraph1 perform(ReadGraph graph) throws DatabaseException {\r
+\r
+ support = graph.getService(SerialisationSupport.class);\r
+\r
+ this.L0 = Layer0.getInstance(graph); \r
+\r
+ long total = System.nanoTime();\r
+\r
+ long startupTime = System.nanoTime();\r
+\r
+ ClusterControl cc = graph.getService(ClusterControl.class);\r
+ \r
+ ids = new TIntIntHashMap();\r
+ values = new TIntObjectHashMap<Variant>();\r
+ \r
+ ArrayList<Resource> rootResources = new ArrayList<Resource>();\r
+ for(Pair<Resource, String> p : configuration.roots) rootResources.add(p.first);\r
+\r
+ Map<Resource, ExtentStatus> preStatus = new HashMap<Resource, ExtentStatus>();\r
+ \r
+ for(Resource root : rootResources) {\r
+ Resource name = graph.getPossibleObject(root, L0.HasName);\r
+ if(name != null) {\r
+ preStatus.put(name, ExtentStatus.EXCLUDED);\r
+ }\r
+ }\r
+ \r
+ for(Resource r : configuration.externals) preStatus.put(r, ExtentStatus.EXTERNAL); \r
+\r
+ long startupTimeEnd = System.nanoTime();\r
+\r
+ long domainTime = System.nanoTime();\r
+ \r
+ String otherStatements = "other" + UUID.randomUUID().toString();\r
+ String valueFileName = "value" + UUID.randomUUID().toString();\r
+ \r
+ File otherStatementsFile = new File(otherStatements);\r
+ File valueFile = new File(valueFileName);\r
+ \r
+ try {\r
+ \r
+ DeferredFileOutputStream otherStatementsStream = new DeferredFileOutputStream(1024*1024, otherStatementsFile);\r
+ DeferredFileOutputStream valueStream = new DeferredFileOutputStream(1024*1024, valueFile);\r
+ \r
+ ObjectOutputStream otherStatementsOutput = new ObjectOutputStream(otherStatementsStream);\r
+ ObjectOutputStream valueOutput = new ObjectOutputStream(valueStream);\r
+\r
+ ClusterState clusterState = cc.getClusterState();\r
+\r
+ TIntHashSet excludedShared = new TIntHashSet();\r
+ \r
+ TreeMap<String, Variant> extensions = new TreeMap<String, Variant>();\r
+ \r
+ Subgraphs.getDomain2(graph, ids, rootResources, preStatus, configuration.specials, otherStatementsOutput, valueOutput, extensions, excludedShared);\r
+ \r
+ id = ids.size();\r
+\r
+ cc.restoreClusterState(clusterState);\r
+\r
+// dumpHeap("domain.hprof");\r
+\r
+ otherStatementsOutput.flush();\r
+ valueOutput.flush();\r
+ otherStatementsStream.close();\r
+ valueStream.close();\r
+ \r
+ long domainDuration = System.nanoTime() - domainTime;\r
+ System.err.println("Analysed graph in " + 1e-9*domainDuration + "s.");\r
+\r
+ internalCount = id;\r
+\r
+ ids.put(support.getTransientId(graph.getResource("http:/")), id++);\r
+ externalNames.add("http:/");\r
+ externalParents.add(-1);\r
+\r
+ InputStream otherStatementsInputStream = null;\r
+ InputStream valueInputStream = null;\r
+ \r
+ if(otherStatementsStream.isInMemory()) {\r
+ otherStatementsInputStream = new ByteArrayInputStream(otherStatementsStream.getData());\r
+ } else {\r
+ otherStatementsInputStream = new FileInputStream(otherStatementsFile);\r
+ }\r
+\r
+ if(valueStream.isInMemory()) {\r
+ valueInputStream = new ByteArrayInputStream(valueStream.getData());\r
+ } else {\r
+ valueInputStream = new FileInputStream(valueFile);\r
+ }\r
+\r
+ otherStatementsStream = null;\r
+ valueStream = null;\r
+ \r
+ ObjectInputStream otherStatementsInput = new ObjectInputStream(otherStatementsInputStream);\r
+ ObjectInputStream valueInput = new ObjectInputStream(valueInputStream);\r
+\r
+ long statementTime = System.nanoTime();\r
+ \r
+ TIntArrayList statementSet = new TIntArrayList();\r
+ \r
+ while(otherStatementsInput.available() > 0) {\r
+ \r
+ int s = otherStatementsInput.readInt();\r
+ \r
+ boolean exclude = !ids.contains(s);\r
+ \r
+ int size = otherStatementsInput.readInt();\r
+ for(int i=0;i<size;i++) {\r
+ int p = otherStatementsInput.readInt();\r
+ int o = otherStatementsInput.readInt();\r
+ if(!exclude) {\r
+ if(excludedShared.contains(o)) {\r
+// System.err.println("excluding shared " + s + " " + p + " " + o);\r
+ } else {\r
+ statementSet.add(s);\r
+ statementSet.add(p);\r
+ statementSet.add(o);\r
+ }\r
+ } else {\r
+// System.err.println("excluding shared " + s);\r
+ }\r
+ }\r
+ \r
+ }\r
+\r
+ TIntIntHashMap inverses = new TIntIntHashMap();\r
+ TIntHashSet predicateSet = new TIntHashSet();\r
+ for(int i=0;i<statementSet.size();i+=3) {\r
+ int p = statementSet.getQuick(i+1);\r
+ if(predicateSet.add(p)) {\r
+ Resource inverse = graph.getPossibleInverse(getResource(p));\r
+ if(inverse != null) inverses.put(p, support.getTransientId(inverse));\r
+ }\r
+ }\r
+ \r
+ predicateSet = null;\r
+ \r
+ TIntArrayList tgStatements = new TIntArrayList();\r
+ \r
+// dumpHeap("export.hprof");\r
+\r
+ // 25%\r
+ int trim = Math.max(65536,statementSet.size()/12);\r
+ \r
+ for(int i=statementSet.size();i>0;i-=3) {\r
+\r
+ if(trim-- == 0) {\r
+ statementSet.remove(i, statementSet.size()-i);\r
+ statementSet.trimToSize();\r
+ trim = Math.max(65536,statementSet.size()/12);\r
+ }\r
+\r
+ int s = statementSet.getQuick(i-3);\r
+ int p = statementSet.getQuick(i-2);\r
+ int o = statementSet.getQuick(i-1);\r
+ \r
+ int subjectId = ids.get(s);\r
+ if(subjectId >= internalCount) System.err.println("Statement for external: " + s + " " + p + " " + o);\r
+ \r
+ int objectId = getId(graph, o, p);\r
+ // The statement can be denied still\r
+ if(objectId != -2) {\r
+ tgStatements.add(subjectId);\r
+ tgStatements.add(getId(graph, p, 0));\r
+ int inverse = inverses.get(p);\r
+ if(inverse != 0) {\r
+ tgStatements.add(getId(graph, inverse, 0));\r
+ } else {\r
+ tgStatements.add(-1);\r
+ }\r
+ tgStatements.add(objectId);\r
+ } else {\r
+ System.out.println("denied");\r
+ }\r
+ \r
+ }\r
+ \r
+ statements = tgStatements.toArray();\r
+\r
+ long statementDuration = System.nanoTime() - statementTime;\r
+ System.err.println("Built transferable statements in " + 1e-9*statementDuration + "s.");\r
+ \r
+ inverses = null;\r
+ \r
+ while(valueInput.available() > 0) {\r
+\r
+ int s = valueInput.readInt();\r
+// Resource subject = support.getResource(s);\r
+ int valueSize = valueInput.readInt();\r
+ byte[] value = new byte[valueSize];\r
+ valueInput.readFully(value);\r
+ Variant variant = (Variant)Bindings.VARIANT.serializer().deserialize(value);\r
+ values.put(s, variant);\r
+ \r
+ }\r
+\r
+ int resourceCount = ids.size();\r
+\r
+ Identity[] identityArray;\r
+ { // Identities\r
+ ArrayList<Identity> identities = new ArrayList<Identity>();\r
+\r
+ for(Pair<Resource, String> r : configuration.roots) {\r
+ Resource type = graph.getPossibleType(r.first, L0.Entity);\r
+ if(type == null) type = L0.Entity;\r
+ identities.add(new Identity(\r
+ ids.get(support.getTransientId(r.first)),\r
+ new Root(r.second, graph.getURI(type))\r
+ ));\r
+ }\r
+\r
+ int internalsPlusExternals = ids.size(); \r
+ for(int i = internalCount; i < internalsPlusExternals ; i++) {\r
+ int parent = externalParents.get(i - internalCount);\r
+ String name = externalNames.get(i - internalCount);\r
+ identities.add(new Identity(\r
+ i, \r
+ new External(parent, name)\r
+ ));\r
+ }\r
+ identityArray = identities.toArray(new Identity[identities.size()]);\r
+ } \r
+ \r
+ final Value[] valueArray = new Value[values.size()];\r
+ { // Values\r
+ values.forEachEntry(new TIntObjectProcedure<Variant>() {\r
+\r
+ int index = 0;\r
+\r
+ @Override\r
+ public boolean execute(int subject, Variant bytes) {\r
+ //if(LOG) log("[VALUE] " + entry.getKey().getResourceId());\r
+ int r = getInternalId(subject);\r
+ if(r==-1) System.err.println("No id for value resource " + subject);\r
+ else valueArray[index++] = new Value(r, bytes);\r
+ return true;\r
+ }\r
+ \r
+ });\r
+ }\r
+ ids = null;\r
+ values = null;\r
+\r
+ TransferableGraph1 result = \r
+ new TransferableGraph1(resourceCount, \r
+ identityArray, \r
+ statements, \r
+ valueArray, extensions);\r
+ \r
+ if(DEBUG) {\r
+ System.out.println("transferable graph content: " + result);\r
+ }\r
+\r
+ long totalEnd = System.nanoTime();\r
+\r
+ if(PROFILE) { \r
+ System.out.println("startup in " + 1e-9*(startupTimeEnd - startupTime) + "s.");\r
+ System.out.println("domain was found in " + 1e-9*(domainDuration) + "s.");\r
+ System.out.println("statements were found in " + 1e-9*(statementDuration) + "s.");\r
+ System.out.println("total time for building subgraph was " + 1e-9*(totalEnd-total) + "s.");\r
+ }\r
+\r
+ return result;\r
+\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ } catch (Throwable t) {\r
+ t.printStackTrace();\r
+ dumpHeap("crash.hprof");\r
+ }\r
+ \r
+ return null;\r
+ \r
+ }\r
+\r
+ private static void dumpHeap(String path) {\r
+ \r
+ try {\r
+ Object bean = getBean();\r
+ if (bean == null)\r
+ return;\r
+\r
+ Method m = bean.getClass().getMethod("dumpHeap", String.class, boolean.class);\r
+ m.invoke(bean, path, true);\r
+ \r
+ } catch (IllegalArgumentException e) {\r
+ } catch (IllegalAccessException e) {\r
+ } catch (SecurityException e) {\r
+ } catch (NoSuchMethodException e) {\r
+ } catch (InvocationTargetException e) {\r
+ } finally {\r
+ }\r
+ \r
+ }\r
+ \r
+ private static Object getBean() {\r
+ Class<?> beanClass = getBeanClass();\r
+ if (beanClass == null)\r
+ return null;\r
+ try {\r
+ Object bean = ManagementFactory.newPlatformMXBeanProxy(\r
+ ManagementFactory.getPlatformMBeanServer(),\r
+ "com.sun.management:type=HotSpotDiagnostic",\r
+ beanClass);\r
+ return bean;\r
+ } catch (IOException e) {\r
+ return null;\r
+ }\r
+ }\r
+ \r
+ private static Class<?> getBeanClass() {\r
+ try {\r
+ Class<?> clazz = Class.forName("com.sun.management.HotSpotDiagnosticMXBean");\r
+ return clazz;\r
+ } catch (ClassNotFoundException e) {\r
+ return null;\r
+ }\r
+ }\r
+ \r
+ \r
+}\r
Code Review / simantics / platform.git / blobdiff