From c3adc8c88589a2b987ea524dd7139bc7da5c7178 Mon Sep 17 00:00:00 2001 From: jsimomaa Date: Wed, 26 Jul 2017 09:40:35 +0300 Subject: [PATCH] Improve PrettyPrintTG performance refs #7383 Change-Id: I4c372679d1049d87a0c8c06ec18228ab826e1510 --- .../graph/representation/PrettyPrintTG.java | 313 +++++----- .../TransferableGraphQueries.java | 205 +++++++ .../TransferableGraphUtils.java | 559 ++++++++++-------- 3 files changed, 674 insertions(+), 403 deletions(-) create mode 100644 bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphQueries.java diff --git a/bundles/org.simantics.graph/src/org/simantics/graph/representation/PrettyPrintTG.java b/bundles/org.simantics.graph/src/org/simantics/graph/representation/PrettyPrintTG.java index 2d4171e1c..cb06d6add 100644 --- a/bundles/org.simantics.graph/src/org/simantics/graph/representation/PrettyPrintTG.java +++ b/bundles/org.simantics.graph/src/org/simantics/graph/representation/PrettyPrintTG.java @@ -11,7 +11,6 @@ import java.nio.file.Paths; import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; import java.util.ArrayList; -import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; @@ -64,6 +63,8 @@ public class PrettyPrintTG { private boolean ignoreIdentifiers; + private TransferableGraphQueries query; + static class ResourceInfo { final boolean hasURI; String name; @@ -104,43 +105,51 @@ public class PrettyPrintTG { } } - public PrettyPrintTG(StringBuilder b, boolean ignoreIdentifiers) throws NoSuchAlgorithmException { + public PrettyPrintTG(TransferableGraph1 tg, StringBuilder b, boolean ignoreIdentifiers) throws NoSuchAlgorithmException { output = b; m = MessageDigest.getInstance("SHA-256"); this.ignoreIdentifiers = ignoreIdentifiers; + + this.query = new TransferableGraphQueries(tg); } - public PrettyPrintTG() throws NoSuchAlgorithmException { - this(new StringBuilder(), false); + public PrettyPrintTG(TransferableGraph1 tg) throws NoSuchAlgorithmException { + this(tg, new StringBuilder(), false); } TreeMap orderedInfos = new TreeMap<>(); TIntObjectHashMap infos = new TIntObjectHashMap<>(); - String tgNodeName(String name) { + private static String tgNodeName(String name) { if (name.contains(" ")) return "\"" + name + "\""; else return name; } - ResourceInfo recurseURI(TransferableGraph1 graph, Identity parent, String parentName, int parentId) { - String name = parentName + "." + tgNodeName(TransferableGraphUtils.getName(parent)); - ResourceInfo info = new ResourceInfo(true, name, parent.resource, parentId); - orderedInfos.put(name, info); - // infos.put(parent.resource, info); - for (Identity child : TransferableGraphUtils.getChildren(graph, parent)) { - recurseURI(graph, child, name, info.resource); - } + private ResourceInfo recurseURI(Map infos, Identity identity, String parentName, int parentId) { + String name = parentName + "." + tgNodeName(TransferableGraphUtils.getName(identity)); + int identityResource = identity.resource; + ResourceInfo info = new ResourceInfo(true, name, identityResource, parentId); + infos.put(name, info); + for (Identity child : query.getChildren(identity)) + recurseURI(infos, child, name, identityResource); return info; } - private TreeMap> sortByPredicateUniqueStatements(TransferableGraph1 graph, int resource) { + /** + * Sorts statements by predicateURI in natural order + * + * @param graph + * @param resource + * @return + */ + private TreeMap> sortByPredicateUniqueStatements(int resource) { TreeMap> results = new TreeMap<>(); - TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource); + TIntArrayList statements = query.getStatements(resource); for (int i = 0; i < statements.size(); i += 2) { int predicate = statements.get(i); - String predicateURI = TransferableGraphUtils.getURI(graph, predicate); + String predicateURI = query.getURI(predicate); TreeSet objects = results.get(predicateURI); if (objects == null) { objects = new TreeSet<>(); @@ -151,32 +160,32 @@ public class PrettyPrintTG { return results; } - void discoverBlank(TransferableGraph1 graph, int resource, TIntArrayList todo) throws Exception { + void discoverBlank(int resource, TIntArrayList todo) throws Exception { // TIntArrayList statements = // TransferableGraphUtils.getStatements(graph, resource); // for(int i=0;i objects : sortByPredicateUniqueStatements(graph, resource).values()) { + for (TreeSet objects : sortByPredicateUniqueStatements(resource).values()) { for (int object : objects) { // int object = statements.get(i+1); - Identity objectId = TransferableGraphUtils.getIdentity(graph, object); + Identity objectId = query.getIdentity(object); if (objectId != null) { if (objectId.definition instanceof External) continue; } - Value value = TransferableGraphUtils.findValue(graph, object); + Value value = query.findValue(object); if (value != null) { infos.put(object, new ResourceInfo(false, printValue(value), object, resource)); - continue; - } - ResourceInfo existing = infos.get(object); - if (existing == null) { - - existing = new ResourceInfo(false, "blank" + blankCounter++, object, resource); - - // System.out.println("created blank" + blankCounter + " - // with object " + object + " resource " + resource); - infos.put(object, existing); - todo.add(object); + } else { + ResourceInfo existing = infos.get(object); + if (existing == null) { + + existing = new ResourceInfo(false, "blank" + blankCounter++, object, resource); + + // System.out.println("created blank" + blankCounter + " + // with object " + object + " resource " + resource); + infos.put(object, existing); + todo.add(object); + } } } } @@ -188,10 +197,10 @@ public class PrettyPrintTG { return new BigInteger(1, m.digest()).toString(16); } - void discoverOwners(TransferableGraph1 graph, ResourceInfo info) { + void discoverOwners(ResourceInfo info) { log("Discovering owners for {}", info); int resource = info.resource; - TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource); + TIntArrayList statements = query.getStatements(resource); for (int i = 0; i < statements.size(); i += 2) { int predicate = statements.get(i); int object = statements.get(i + 1); @@ -201,7 +210,7 @@ public class PrettyPrintTG { // Check if predicate is inverse, this just resolves all // predicates to be inverse with ending "Inverse".. - String predicateUri = rewritePredicateURI(graph, predicate); + String predicateUri = rewritePredicateURI(predicate); if (!predicateUri.endsWith("Inverse") && !predicateUri.endsWith("Of")) { existing.ownedResourcesWithPredicates.put(resource, predicate); // if (predicateUri.endsWith("Of")) { @@ -241,7 +250,7 @@ public class PrettyPrintTG { } } - public static String getExternalURI(TransferableGraph1 tg, External ext) { + public String getExternalURI(External ext) { String name = ext.name; if (name.contains(" ")) name = name.replace(" ", "_").replaceAll("@", "_");// name = "\"" + @@ -249,9 +258,9 @@ public class PrettyPrintTG { int parentId = ext.parent; // if(parentId == 0) return ext.name; // else { - Identity id = TransferableGraphUtils.getIdentity(tg, parentId); + Identity id = query.getIdentity(parentId); if (id.definition instanceof External) { - return getExternalURI(tg, (External) id.definition) + "/" + name; + return getExternalURI((External) id.definition) + "/" + name; } else if (id.definition instanceof Root) { Root root = (Root) id.definition; return "http:/" + root.name + "/" + name; @@ -261,20 +270,20 @@ public class PrettyPrintTG { // } } - public static String getExternalURI(TransferableGraph1 tg, int resource) { - Identity id = TransferableGraphUtils.getIdentity(tg, resource); + public String getExternalURI(int resource) { + Identity id = query.getIdentity(resource); if (id == null) return null; if (id.definition instanceof External) { External ext = (External) id.definition; - return getExternalURI(tg, ext); + return getExternalURI(ext); } return null; } - String rewritePredicateURI(TransferableGraph1 graph, int predicate) { + String rewritePredicateURI(int predicate) { - String uri = getExternalURI(graph, predicate); + String uri = getExternalURI(predicate); if (uri == null) { ResourceInfo info = infos.get(predicate); if (info != null) @@ -301,7 +310,7 @@ public class PrettyPrintTG { output.append(" "); } - String printBlank(TransferableGraph1 graph, String predicateURI2, ResourceInfo info, int indent) { + String printBlank(String predicateURI2, ResourceInfo info, int indent) { if (info.hasURI) return null; @@ -328,7 +337,7 @@ public class PrettyPrintTG { if (info.ownedResourcesWithPredicates.isEmpty()) { if (DEBUG) System.out.print("printBlank"); - String uri = printURI(graph, info, false, indent, false); + String uri = printURI(info, false, indent, false); if (uri != null) output.append(uri); } @@ -354,14 +363,14 @@ public class PrettyPrintTG { return ((predicate & 0xffffffffL) << 32) | (object & 0xffffffffL); } - private void addInlineStatement(TransferableGraph1 graph, Map> statements, String predicate, + private void addInlineStatement(Map> statements, String predicate, ResourceInfo objectInfo, int indent) { Set objects = statements.get(predicate); if (objects == null) { objects = new TreeSet<>(); statements.put(predicate, objects); } - String uri = printURI(graph, objectInfo, false, indent + 1, true); + String uri = printURI(objectInfo, false, indent + 1, true); if (uri != null) { // TODO: this is not the right place to remove trailing newline uri = uri.endsWith("\n") ? uri.substring(0, uri.length() - 2) : uri; @@ -382,7 +391,7 @@ public class PrettyPrintTG { objects.add(object); } - String printURI(TransferableGraph1 graph, ResourceInfo info, boolean requireURI, int indent, boolean inline) { + String printURI(ResourceInfo info, boolean requireURI, int indent, boolean inline) { if (requireURI && !info.hasURI) return null; @@ -393,8 +402,7 @@ public class PrettyPrintTG { return null; Map> statements = new TreeMap<>(); - Identity consistsOf = TransferableGraphUtils.findExternal(graph, - "http://www.simantics.org/Layer0-1.1/ConsistsOf"); + Identity consistsOf = query.findExternalByURI("http://www.simantics.org/Layer0-1.1/ConsistsOf"); // Identity partOf = TransferableGraphUtils.findExternal(graph, // "http://www.simantics.org/Layer0-1.1/PartOf"); TLongHashSet processed = new TLongHashSet(); @@ -410,9 +418,9 @@ public class PrettyPrintTG { processed.add(stmId); } - TreeMap predicateURIs = new TreeMap<>(); + TreeMap> predicateURIs = new TreeMap<>(); - TIntArrayList rawStatements = TransferableGraphUtils.getStatements(graph, info.resource); + TIntArrayList rawStatements = query.getStatements(info.resource); if (DEBUG) System.out.println( "rawStatements size for " + info.name + " : " + rawStatements.size() + " " + rawStatements); @@ -442,32 +450,38 @@ public class PrettyPrintTG { // indent++; // } } - String predicateURI = rewritePredicateURI(graph, predicate); - predicateURIs.put(predicateURI, object); + String predicateURI = rewritePredicateURI(predicate); + List objects = predicateURIs.get(predicateURI); + if (objects == null) { + objects = new ArrayList<>(); + predicateURIs.put(predicateURI, objects); + } + objects.add(object); } - for (Entry entry : predicateURIs.entrySet()) { + for (Entry> entry : predicateURIs.entrySet()) { String predicateURI = entry.getKey(); - int object = entry.getValue(); - - ResourceInfo objectInfo = infos.get(object); - if (objectInfo == null) { - String objectURI = rewritePredicateURI(graph, object); - if (DEBUG) - System.out.println(" adding statement " + predicateURI + " " + objectURI); - addStatement(statements, predicateURI, objectURI); - } else if (objectInfo.ownedBy.size() == 1 && objectInfo.ownedBy.contains(info)) { - // inline printing with _ - if (DEBUG) - System.out.println(" adding inline statement " + predicateURI + " " + objectInfo.name); - addInlineStatement(graph, statements, predicateURI, objectInfo, indent); - } else { - String objectName = objectInfo.name; - if (objectName.startsWith("blank")) { - objectName = getBlankRewrite(objectName); + List objects = entry.getValue(); + for (int object : objects) { + ResourceInfo objectInfo = infos.get(object); + if (objectInfo == null) { + String objectURI = rewritePredicateURI(object); + if (DEBUG) + System.out.println(" adding statement " + predicateURI + " " + objectURI); + addStatement(statements, predicateURI, objectURI); + } else if (objectInfo.ownedBy.size() == 1 && objectInfo.ownedBy.contains(info)) { + // inline printing with _ + if (DEBUG) + System.out.println(" adding inline statement " + predicateURI + " " + objectInfo.name); + addInlineStatement(statements, predicateURI, objectInfo, indent); + } else { + String objectName = objectInfo.name; + if (objectName.startsWith("blank")) { + objectName = getBlankRewrite(objectName); + } + if (DEBUG) + System.out.println(" adding statement " + predicateURI + " " + objectName); + addStatement(statements, predicateURI, objectName); } - if (DEBUG) - System.out.println(" adding statement " + predicateURI + " " + objectName); - addStatement(statements, predicateURI, objectName); } } @@ -547,46 +561,37 @@ public class PrettyPrintTG { } } - TreeMap ownedOrdered = new TreeMap<>(); + TreeMap> ownedOrdered = new TreeMap<>(); for (int i = 0; i < info.owned.size(); i += 2) { - String predicateURI = rewritePredicateURI(graph, info.owned.get(i)); - ownedOrdered.put(predicateURI, info.owned.get(i + 1)); + String predicateURI = rewritePredicateURI(info.owned.get(i)); + Set owneds = ownedOrdered.get(predicateURI); + if (owneds == null) { + owneds = new TreeSet<>(); + ownedOrdered.put(predicateURI, owneds); + } + owneds.add(info.owned.get(i + 1)); } if (DEBUG) System.out.println(info.name + " : " + ownedOrdered.keySet()); - for (Entry entry : ownedOrdered.entrySet()) { + for (Entry> entry : ownedOrdered.entrySet()) { String predicateURI = entry.getKey(); - int owned = entry.getValue(); - ResourceInfo ownedInfo = infos.get(owned); - - String blank = printBlank(graph, predicateURI, ownedInfo, indent + 1); - if (blank != null) { - output.append(blank); + Set owneds = entry.getValue(); + for (int owned : owneds) { + ResourceInfo ownedInfo = infos.get(owned); + + String blank = printBlank(predicateURI, ownedInfo, indent + 1); + if (blank != null) { + output.append(blank); + } } } return output.toString(); } - void prettyPrint(Path input, Path output) throws Exception { - - System.out.format("Converting exported shared ontology%n\t" + input.toString() - + "%nto bundle-compatible ontology%n\t" + output.toString()); - try (InputStream is = new BufferedInputStream(Files.newInputStream(input), 128 * 1024)) { - DataInput dis = new DataInputStream(is); - org.simantics.databoard.container.DataContainer container = DataContainers.readFile(dis); - Binding binding = TransferableGraph1.BINDING; - TransferableGraph1 graph = (TransferableGraph1) container.content.getValue(binding); - prettyPrint(graph); - Files.write(output, this.output.toString().getBytes()); - - } - - } - static Map knownOntologies = new HashMap<>(); static { @@ -607,26 +612,26 @@ public class PrettyPrintTG { knownOntologies.put("http://www.semantum.fi/SimupediaWorkbench-1.0", "SIMUPEDIA_WORKBENCH"); } - void prettyPrint(TransferableGraph1 graph) throws Exception { + void prettyPrint() throws Exception { log("Starting prettyPrint for TransferableGraph with {} resources, {} identities, {} statements and {} values", - graph.resourceCount, graph.identities, graph.statements.length, graph.values.length); + query.getGraph().resourceCount, query.getGraph().identities, query.getGraph().statements.length, query.getGraph().values.length); - for (Identity id : graph.identities) { + query.forIdentities(id -> { + int identityResource = id.resource; if (id.definition instanceof Internal) { Internal internal = (Internal) id.definition; - Identity parent = TransferableGraphUtils.getIdentity(graph, internal.parent); - if (parent.definition instanceof External) { + Identity parent = query.getIdentity(internal.parent); + if (parent.definition instanceof External || parent.definition instanceof Root) { log("Resolving internal identity {}", id); String name = "BASE"; - ResourceInfo info = new ResourceInfo(true, name, id.resource, -1); - info.aliasURI = TransferableGraphUtils.getURI(graph, id.resource); + ResourceInfo info = new ResourceInfo(true, name, identityResource, -1); + info.aliasURI = query.getURI(identityResource); info.newResource = true; orderedInfos.put(name, info); // infos.put(id.resource, info); log(" which parent is external {} and has an aliasURI {}", parent, info.aliasURI); - for (Identity child : TransferableGraphUtils.getChildren(graph, id)) { - recurseURI(graph, child, name, info.resource); - } + for (Identity child : query.getChildren(id)) + recurseURI(orderedInfos, child, name, identityResource); log(" and has {} children", infos.size()); } } else if (id.definition instanceof External) { @@ -640,7 +645,7 @@ public class PrettyPrintTG { String prefix = ext.name.substring(0, index); int index2 = ext.name.indexOf('/', index); String ontology = index2 == -1 ? ext.name : ext.name.substring(0, index2); - String uri = TransferableGraphUtils.getURI(graph, id.resource); + String uri = query.getURI(identityResource); log(" which was resolved as URI={} and prefix={}", uri, prefix); @@ -648,7 +653,7 @@ public class PrettyPrintTG { } else if (ext.name.contains("-")) { log("Resolving possible ontology {}", ext); - String uri = TransferableGraphUtils.getURI(graph, id.resource); + String uri = query.getURI(identityResource); Matcher m = versionExtractPattern.matcher(uri); if (m.matches()) { if (!ontologies.containsKey(uri)) { @@ -660,7 +665,8 @@ public class PrettyPrintTG { } } } - } + return true; + }); // Discover other resources log("Discovering other resources.."); @@ -675,10 +681,10 @@ public class PrettyPrintTG { while (!todo.isEmpty()) { int resource = todo.removeAt(todo.size() - 1); - discoverBlank(graph, resource, todo); + discoverBlank(resource, todo); } for (ResourceInfo info : infos.valueCollection()) - discoverOwners(graph, info); + discoverOwners(info); // for(ResourceInfo info : infos.valueCollection()) // fixInstanceOf(graph, info); @@ -697,12 +703,15 @@ public class PrettyPrintTG { @Override public boolean execute(int owner, int predicate) { + ResourceInfo ownerInfo = infos.get(owner); ownerInfo.owned.add(predicate); ownerInfo.owned.add(info.resource); return false; } }); + } else { + System.err.println("Here we are with " + info); } } @@ -717,21 +726,18 @@ public class PrettyPrintTG { } } - Identity routeGraphConn = TransferableGraphUtils.findExternal(graph, - "http://www.simantics.org/Diagram-2.2/RouteGraphConnection"); - Identity instanceOf = TransferableGraphUtils.findExternal(graph, - "http://www.simantics.org/Layer0-1.1/InstanceOf"); - Identity diagramConnetionToConnection = TransferableGraphUtils.findExternal(graph, - "http://www.simantics.org/Modeling-1.2/DiagramConnectionToConnection"); + Identity routeGraphConn = query.findExternalByURI("http://www.simantics.org/Diagram-2.2/RouteGraphConnection"); + Identity instanceOf = query.findExternalByURI("http://www.simantics.org/Layer0-1.1/InstanceOf"); + Identity diagramConnetionToConnection = query.findExternalByURI("http://www.simantics.org/Modeling-1.2/DiagramConnectionToConnection"); + Identity elemTo = query.findExternalByURI("http://www.simantics.org/Modeling-1.2/ElementToComponent"); for (ResourceInfo infoo : infos.valueCollection()) { - Identity elemTo = TransferableGraphUtils.findExternal(graph, "http://www.simantics.org/Modeling-1.2/ElementToComponent"); if (elemTo != null) { - int elemToComponent = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource, elemTo); + int elemToComponent = query.getPossibleObject(infoo.resource, elemTo); if (elemToComponent != TransferableGraphUtils.NOT_FOUND) { - Identity component = TransferableGraphUtils.getIdentity(graph, elemToComponent); - Identity internal = TransferableGraphUtils.getIdentity(graph, infoo.resource); + Identity component = query.getIdentity(elemToComponent); + Identity internal = query.getIdentity(infoo.resource); if (internal.definition instanceof Internal && component.definition instanceof Internal) { Internal iComponent = (Internal) component.definition; infoo.name = infoo.name.substring(0, infoo.name.lastIndexOf(".") + 1) + iComponent.name; @@ -740,29 +746,29 @@ public class PrettyPrintTG { } if (instanceOf != null) { - int instOf = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource, instanceOf); + int instOf = query.getPossibleObject( infoo.resource, instanceOf); if (instOf != TransferableGraphUtils.NOT_FOUND && routeGraphConn != null) { if (instOf == routeGraphConn.resource) { // Found routegraphconnection, change name // Lets go to configuration - int connection = TransferableGraphUtils.getPossibleObject2(graph, infoo.resource, + int connection = query.getPossibleObject( infoo.resource, diagramConnetionToConnection); if (connection != TransferableGraphUtils.NOT_FOUND) { // Gather all inverse statements to construct unique // name List nameParts = new ArrayList<>(); - TIntArrayList statements = TransferableGraphUtils.getStatements(graph, connection); + TIntArrayList statements = query.getStatements(connection); for (int i = 0; i < statements.size(); i += 2) { int predicate = statements.get(i); - Identity possibleInverse = TransferableGraphUtils.getIdentity(graph, predicate); + Identity possibleInverse = query.getIdentity(predicate); if (possibleInverse != null) { int inverseRelation = TransferableGraphUtils.NOT_FOUND; int parentId = TransferableGraphUtils.NOT_FOUND; if (possibleInverse.definition instanceof Internal) { Internal iPossibleInverse = (Internal) possibleInverse.definition; if (iPossibleInverse.name.equals("Inverse")) { - inverseRelation = TransferableGraphUtils.getPossibleObject2(graph, + inverseRelation = query.getPossibleObject( connection, possibleInverse); parentId = iPossibleInverse.parent; } else { @@ -771,7 +777,7 @@ public class PrettyPrintTG { } else if (possibleInverse.definition instanceof External) { External ePossibleInverse = (External) possibleInverse.definition; if (ePossibleInverse.name.equals("Inverse")) { - inverseRelation = TransferableGraphUtils.getPossibleObject2(graph, + inverseRelation = query.getPossibleObject( connection, possibleInverse); parentId = ePossibleInverse.parent; } else { @@ -782,8 +788,8 @@ public class PrettyPrintTG { } if (inverseRelation != TransferableGraphUtils.NOT_FOUND) { // Ok found something - Identity object = TransferableGraphUtils.getIdentity(graph, inverseRelation); - Identity parent = TransferableGraphUtils.getIdentity(graph, parentId); + Identity object = query.getIdentity(inverseRelation); + Identity parent = query.getIdentity(parentId); String objectName, parentName; if (object.definition instanceof Internal) { objectName = ((Internal) object.definition).name; @@ -818,7 +824,6 @@ public class PrettyPrintTG { infoo.name = infoo.name.substring(0, infoo.name.lastIndexOf(".") + 1) + name; } else { LOGGER.error("Could not find connection for " + infoo + ". Statements of graph below"); - LOGGER.error(Arrays.toString(graph.statements)); LOGGER.error("Subject -> Predicate : " + infoo.resource + " -> " + diagramConnetionToConnection.resource); } @@ -828,7 +833,7 @@ public class PrettyPrintTG { } for (ResourceInfo info : infos.valueCollection()) { if (info.name.startsWith("blank")) { - info.name = "blank" + findHash(graph, info); + info.name = "blank" + findHash(info); } } @@ -839,7 +844,7 @@ public class PrettyPrintTG { for (ResourceInfo info : order.values()) { if (DEBUG) System.out.print("info "); - String uri = printURI(graph, info, true, 0, false); + String uri = printURI(info, true, 0, false); if (uri != null) output.append(uri); } @@ -854,7 +859,7 @@ public class PrettyPrintTG { // These will be printed later rblanks.put(getBlankRewrite(info.name), info); } else { - String uri = printURI(graph, info, false, 0, false); + String uri = printURI(info, false, 0, false); if (uri != null) output.append(uri); } @@ -865,7 +870,7 @@ public class PrettyPrintTG { if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) { if (DEBUG) System.out.print("ownedResources "); - String uri = printURI(graph, info, false, 0, false); + String uri = printURI(info, false, 0, false); if (uri != null) output.append(uri); } @@ -886,7 +891,7 @@ public class PrettyPrintTG { } - private String calculateHash(TransferableGraph1 graph, ResourceInfo info) { + private String calculateHash(ResourceInfo info) { StringBuilder statementHash = new StringBuilder(); TreeSet parts = new TreeSet<>(); for (int i = 0; i < info.owned.size(); i += 2) { @@ -895,7 +900,7 @@ public class PrettyPrintTG { // Lets resolve a unique name for this based on the statements this // one has - String predicatee = rewritePredicateURI(graph, predicate); + String predicatee = rewritePredicateURI(predicate); ResourceInfo objInfo = infos.get(object); parts.add(predicatee + "->" + objInfo.name + ";;;"); } @@ -921,14 +926,14 @@ public class PrettyPrintTG { return hash; } - private String findHash(TransferableGraph1 graph, ResourceInfo info) { + private String findHash(ResourceInfo info) { if (info.name.startsWith("blank")) { String hash = hashes.get(info.name); if (hash == null) { String oldName = info.name; if (DEBUG) System.out.print("calculating hash for " + oldName + " "); - hash = calculateHash(graph, info); + hash = calculateHash(info); if (hashes.put(oldName, hash) != null) { System.err.println("!!!!A clash occured for " + info + " with hash " + hash); } @@ -943,19 +948,31 @@ public class PrettyPrintTG { public static String print(TransferableGraph1 tg, boolean ignoreIdentifiers) throws Exception { StringBuilder b = new StringBuilder(); - new PrettyPrintTG(b, ignoreIdentifiers).prettyPrint(tg); + new PrettyPrintTG(tg, b, ignoreIdentifiers).prettyPrint(); return b.toString(); } public static void main(String[] args) throws Exception { if (args.length < 1) { System.out.println("Required arguments: []"); - } else if (args.length < 2) { - Path input = Paths.get(args[0]); - Path output = input.getParent().resolve(input.getName(input.getNameCount() - 1) + ".fixed"); - new PrettyPrintTG().prettyPrint(input, output); + } + Path input; + Path output; + if (args.length < 2) { + input = Paths.get(args[0]); + output = input.getParent().resolve(input.getName(input.getNameCount() - 1) + ".fixed"); } else { - new PrettyPrintTG().prettyPrint(Paths.get(args[0]), Paths.get(args[1])); + input = Paths.get(args[0]); + output = Paths.get(args[1]); + } + System.out.format("Converting exported shared ontology%n\t" + input.toString() + + "%nto bundle-compatible ontology%n\t" + output.toString()); + try (InputStream is = new BufferedInputStream(Files.newInputStream(input), 128 * 1024)) { + DataInput dis = new DataInputStream(is); + org.simantics.databoard.container.DataContainer container = DataContainers.readFile(dis); + Binding binding = TransferableGraph1.BINDING; + TransferableGraph1 graph = (TransferableGraph1) container.content.getValue(binding); + new PrettyPrintTG(graph).prettyPrint(); } } diff --git a/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphQueries.java b/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphQueries.java new file mode 100644 index 000000000..5d4c1850b --- /dev/null +++ b/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphQueries.java @@ -0,0 +1,205 @@ +package org.simantics.graph.representation; + +import java.util.Comparator; +import java.util.Set; +import java.util.TreeMap; +import java.util.TreeSet; + +import gnu.trove.impl.Constants; +import gnu.trove.list.array.TIntArrayList; +import gnu.trove.map.hash.TIntObjectHashMap; +import gnu.trove.map.hash.TObjectIntHashMap; +import gnu.trove.procedure.TObjectProcedure; + +public class TransferableGraphQueries { + + private static final int NOT_FOUND = TransferableGraphUtils.NOT_FOUND; + + private final TransferableGraph1 tg; + + private final TIntObjectHashMap internalIdentities = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, NOT_FOUND); + private final TIntObjectHashMap externalIdentities = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, NOT_FOUND); + private final TIntObjectHashMap rootIdentities = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, NOT_FOUND); + + private final TObjectIntHashMap internalIdentitiesByURI = new TObjectIntHashMap<>(); + private final TObjectIntHashMap externalIdentitiesByURI = new TObjectIntHashMap<>(); + private final TObjectIntHashMap rootIdentitiesByURI = new TObjectIntHashMap<>(); + + private final TIntObjectHashMap statementsCache = new TIntObjectHashMap<>(Constants.DEFAULT_CAPACITY, Constants.DEFAULT_LOAD_FACTOR, NOT_FOUND); + + public TransferableGraphQueries(TransferableGraph1 graph) { + this.tg = graph; + + // Calculate internals + initializeIdentities(); + } + + private void initializeIdentities() { + for (Identity identity : tg.identities) { + IdentityDefinition definition = identity.definition; + if (definition instanceof Internal) { + Internal internal = (Internal) definition; + internalIdentities.put(identity.resource, identity); + internalIdentitiesByURI.put(getURI(identity), identity.resource); + } else if (definition instanceof External) { + External external = (External) definition; + externalIdentities.put(identity.resource, identity); + externalIdentitiesByURI.put(getURI(identity), identity.resource); + } else if (definition instanceof Root) { + Root root = (Root) definition; + rootIdentities.put(identity.resource, identity); + rootIdentitiesByURI.put(getURI(identity), identity.resource); + } + } + } + + public String getURI(Identity identity) { + IdentityDefinition definition = identity.definition; + if(definition instanceof External) { + External def = (External)definition; + if(def.parent == -1) return "http:/"; + else return getURI(def.parent) + "/" + def.name; + } else if(definition instanceof Root) { + Root def = (Root)definition; + if(def.name.isEmpty()) return "http:/"; + return def.name; + } else if (definition instanceof Internal) { + Internal def = (Internal)definition; + return getURI(def.parent) + "/" + def.name; + } else { + return ""; + } + } + + public String getURI(int id) { + Identity identity = getIdentity(id); + if (identity == null) + return ":"; + return getURI(identity); + } + + private static final Comparator IDENTITY_NAME_COMPARATOR = new Comparator() { + + @Override + public int compare(Identity o1, Identity o2) { + if (o1.definition instanceof Internal && o2.definition instanceof Internal) { + Internal i1 = (Internal) o1.definition; + Internal i2 = (Internal) o2.definition; + return i1.name.compareTo(i2.name); + } else if (o1.definition instanceof External && o2.definition instanceof External) { + External e1 = (External) o1.definition; + External e2 = (External) o2.definition; + return e1.name.compareTo(e2.name); + } else { + throw new IllegalArgumentException(o1 + " " + o2); + } + } + }; + + public Set getChildren(Identity parent) { + TreeSet children = new TreeSet<>(IDENTITY_NAME_COMPARATOR); + internalIdentities.forEachEntry((resource, identity) -> { + Internal internal = (Internal) identity.definition; + if (internal.parent == parent.resource) + children.add(identity); + return true; + }); + + return children; + } + + public Identity findInternalByName(String name) { + int internal = internalIdentitiesByURI.get(name); + if (internal == NOT_FOUND) + return null; + return internalIdentities.get(internal); + } + + private Identity findExternalByName(String name) { + int external = externalIdentitiesByURI.get(name); + if (external == NOT_FOUND) + return null; + return externalIdentities.get(external); + } + + private Identity findExternalByNameAndParent(String name, int parent) { + Identity external = findExternalByName(name); + if (external.resource == parent) + return external; + return null; + } + + public Identity findExternalByURI(String uri) { + int v = externalIdentitiesByURI.get(uri); + if (v == NOT_FOUND) + return null; + return externalIdentities.get(v); + } + + public Identity findRootByName(String name) { + int root = rootIdentitiesByURI.get(name); + if (root == NOT_FOUND) + return null; + return rootIdentities.get(root); + } + + public String getName(Identity identity) { + return TransferableGraphUtils.getName(identity); + } + + public void forIdentities(TObjectProcedure procedure) { + for (Identity identity : tg.identities) { + if (!procedure.execute(identity)) { + break; + } + } + } + + public Identity getIdentity(int resource) { + Identity result = rootIdentities.get(resource); + if (result == null) + result = externalIdentities.get(resource); + if (result == null) + result = internalIdentities.get(resource); + return result; + } + + public Value findValue(int object) { + return TransferableGraphUtils.findValue(tg, object); + } + + public TreeMap> sortByPredicateUniqueStatements(int resource) { + TreeMap> results = new TreeMap<>(); + TIntArrayList statements = getStatements(resource); + for (int i = 0; i < statements.size(); i += 2) { + int predicate = statements.get(i); + String predicateURI = getURI(predicate); + TreeSet objects = results.get(predicateURI); + if (objects == null) { + objects = new TreeSet<>(); + } + objects.add(statements.get(i + 1)); + results.put(predicateURI, objects); + } + return results; + } + + public TIntArrayList getStatements(int resource) { +// System.out.println("getting statements with " + resource); + TIntArrayList statements = statementsCache.get(resource); + if (statements == null) { + statements = TransferableGraphUtils.getStatements(tg, resource); + statementsCache.put(resource, statements); + } + return statements; + } + + public int getPossibleObject(int subject, Identity predicate) { + return TransferableGraphUtils.getPossibleObject2(tg, subject, predicate); + } + + public TransferableGraph1 getGraph() { + return tg; + } + +} diff --git a/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphUtils.java b/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphUtils.java index b210d8dd7..10637ad65 100644 --- a/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphUtils.java +++ b/bundles/org.simantics.graph/src/org/simantics/graph/representation/TransferableGraphUtils.java @@ -16,156 +16,205 @@ import gnu.trove.map.hash.TIntObjectHashMap; public class TransferableGraphUtils { - public static Collection getRoots(TransferableGraph1 tg) { - - ArrayList result = new ArrayList(); - for(Identity id : tg.identities) { - if(id.definition instanceof Root) result.add(id); - } - return result; - - } - - public static Identity findRootWithName(TransferableGraph1 tg, String name) { - - for(Identity id : tg.identities) { - if(id.definition instanceof Root) { - Root ext = (Root)id.definition; - if(ext.name.equals(name)) return id; - } - } - return null; - - } + public static Collection getRoots(TransferableGraph1 tg) { + + ArrayList result = new ArrayList(); + for(Identity id : tg.identities) { + if(id.definition instanceof Root) result.add(id); + } + return result; + + } + + public static Identity findRootWithName(TransferableGraph1 tg, String name) { + + for(Identity id : tg.identities) { + if(id.definition instanceof Root) { + Root ext = (Root)id.definition; + if(ext.name.equals(name)) return id; + } + } + return null; + + } - public static Identity findExternalWithName(TransferableGraph1 tg, String name) { - - for(Identity id : tg.identities) { - if(id.definition instanceof External) { - External ext = (External)id.definition; - if(ext.name.equals(name)) return id; - } - } - return null; - - } + public static Identity findExternalWithName(TransferableGraph1 tg, String name) { + + for(Identity id : tg.identities) { + if(id.definition instanceof External) { + External ext = (External)id.definition; + if(ext.name.equals(name)) return id; + } + } + return null; + + } + + public static Identity findExternalWithNameAndParent(TransferableGraph1 tg, int parent, String name) { + + for(Identity id : tg.identities) { + if(id.definition instanceof External) { + External ext = (External)id.definition; + if(ext.name.equals(name) && ext.parent == parent) return id; + } + } + return null; + + } + + public static Identity findExternal(TransferableGraph1 tg, String uri) { + + Identity identity = findExternalWithName(tg, "http:/"); + if(identity == null) identity = findExternalWithName(tg, ""); + if(identity == null) identity = findRootWithName(tg, ""); + if("http:/".equals(uri)) return identity; + String[] tokens = uri.substring("http://".length()).split("/"); + for(String token : tokens) { + identity = findExternalWithNameAndParent(tg, identity.resource, token); + if (identity == null) { + return null; + } + } + return identity; + + } + + public static Identity getIdentity(TransferableGraph1 tg, int resource) { + for(Identity id : tg.identities) { + if(id.resource == resource) return id; + } + return null; + } + + public static TIntArrayList getStatements(TransferableGraph1 tg, int resource) { + TIntArrayList result = new TIntArrayList(); + for(int i=0;i getChildren2(TransferableGraph1 tg, Identity parent) { + return getChildren2(tg, parent.resource); + } + + public static Collection getChildren2(TransferableGraph1 tg, int parentResource) { + TreeMap result = new TreeMap<>(); + for (Identity id : tg.identities) { + if (id.definition instanceof Internal) { + Internal internal = (Internal) id.definition; + if (internal.parent == parentResource) + result.put(internal.name, id); + } + } + Identity consistsOf = findExternal(tg, "http://www.simantics.org/Layer0-1.1/ConsistsOf"); + Identity hasName = findExternal(tg, "http://www.simantics.org/Layer0-1.1/HasName"); + for (int i = 0; i < tg.statements.length; i += 4) { + if (tg.statements[i] == parentResource) { + if (tg.statements[i + 1] == consistsOf.resource) { + Identity identity = getIdentity(tg, tg.statements[i + 3]); + if (identity != null) { + if (identity.definition instanceof Internal) { + Internal internal = (Internal) identity.definition; + result.put(internal.name, identity); + } + } else { + int possibleNameResource = getPossibleObject2(tg, tg.statements[i + 3], hasName); + if (possibleNameResource != NOT_FOUND) { + Value value = findValue(tg, possibleNameResource); + if (value != null) { + try { + String name = (String) value.value.getValue(Bindings.STRING); + result.put(name, new Identity(tg.statements[i + 3], new Internal(tg.statements[i], name))); + } catch (AdaptException e) { + e.printStackTrace(); + } + } + } + } + } + } + } + return result.values(); + } - public static Identity findExternalWithNameAndParent(TransferableGraph1 tg, int parent, String name) { - - for(Identity id : tg.identities) { - if(id.definition instanceof External) { - External ext = (External)id.definition; - if(ext.name.equals(name) && ext.parent == parent) return id; - } - } - return null; - - } - - public static Identity findExternal(TransferableGraph1 tg, String uri) { - - Identity identity = findExternalWithName(tg, "http:/"); - if(identity == null) identity = findExternalWithName(tg, ""); - if(identity == null) identity = findRootWithName(tg, ""); - if("http:/".equals(uri)) return identity; - String[] tokens = uri.substring("http://".length()).split("/"); - for(String token : tokens) { - identity = findExternalWithNameAndParent(tg, identity.resource, token); - if (identity == null) { - return null; - } - } - return identity; - - } - - public static Identity getIdentity(TransferableGraph1 tg, int resource) { - for(Identity id : tg.identities) { - if(id.resource == resource) return id; - } - return null; - } - - public static TIntArrayList getStatements(TransferableGraph1 tg, int resource) { - TIntArrayList result = new TIntArrayList(); - for(int i=0;i getChildren(TransferableGraph1 tg, Identity parent) { - TreeMap result = new TreeMap<>(); - for(Identity id : tg.identities) { - if(id.definition instanceof Internal) { - Internal internal = (Internal)id.definition; - if(internal.parent == parent.resource) result.put(internal.name, id); - } - } - Identity consistsOf = findExternal(tg, "http://www.simantics.org/Layer0-1.1/ConsistsOf"); - Identity hasName = findExternal(tg, "http://www.simantics.org/Layer0-1.1/HasName"); - for(int i=0;i getChildren(TransferableGraph1 tg, Identity parent) { + TreeMap result = new TreeMap<>(); + for(Identity id : tg.identities) { + if(id.definition instanceof Internal) { + Internal internal = (Internal)id.definition; + if(internal.parent == parent.resource) result.put(internal.name, id); + } + } + Identity consistsOf = findExternal(tg, "http://www.simantics.org/Layer0-1.1/ConsistsOf"); + Identity hasName = findExternal(tg, "http://www.simantics.org/Layer0-1.1/HasName"); + for(int i=0;i getNames(TransferableGraph1 tg, Collection ids) { - Map result = new HashMap(); - for(Identity id : ids) { - if(id.definition instanceof Internal) { - Internal internal = (Internal)id.definition; - result.put(id, internal.name); - } - } - return result; - } + public static Map getNames(TransferableGraph1 tg, Collection ids) { + Map result = new HashMap(); + for(Identity id : ids) { + if(id.definition instanceof Internal) { + Internal internal = (Internal)id.definition; + result.put(id, internal.name); + } + } + return result; + } - public static String getName(TransferableGraph1 tg, Identity id) { - return getName(id); - } + public static String getName(TransferableGraph1 tg, Identity id) { + return getName(id); + } - public static String getName(Identity id) { - if(id.definition instanceof Internal) { - Internal internal = (Internal)id.definition; - return internal.name; - } else if(id.definition instanceof External) { - External external = (External)id.definition; - return external.name; - } else if(id.definition instanceof Root) { - Root root = (Root)id.definition; - return root.name; - } else { - Optional optional = (Optional)id.definition; - return optional.name; - } - } + public static String getName(Identity id) { + if(id.definition instanceof Internal) { + Internal internal = (Internal)id.definition; + return internal.name; + } else if(id.definition instanceof External) { + External external = (External)id.definition; + return external.name; + } else if(id.definition instanceof Root) { + Root root = (Root)id.definition; + return root.name; + } else { + Optional optional = (Optional)id.definition; + return optional.name; + } + } - public static String getRootType(Identity id) { - if(id.definition instanceof Root) { - Root root = (Root)id.definition; - return root.type; - } else { - throw new IllegalArgumentException("Expected root, got " + id); - } - } + public static String getRootType(Identity id) { + if(id.definition instanceof Root) { + Root root = (Root)id.definition; + return root.type; + } else { + throw new IllegalArgumentException("Expected root, got " + id); + } + } - public static Value findValue(TransferableGraph1 tg, int subject) { - for(Value v : tg.values) { - if(v.resource == subject) return v; - } - return null; - } - - public static String getURI(TransferableGraph1 tg, int id) { - return getURI(tg.resourceCount, tg.identities, id); - } - - public static String getURI(int resourceCount, Identity[] identities, int id) { - for(Identity identity : identities) { - if(identity.resource == id) { - IdentityDefinition definition = identity.definition; - if(definition instanceof External) { - External def = (External)definition; - if(def.parent == -1) return "http:/"; - else return getURI(resourceCount, identities, def.parent) + "/" + def.name; - } else if(definition instanceof Root) { - Root def = (Root)definition; - if(def.name.isEmpty()) return "http:/"; - return def.name; - } else if (definition instanceof Internal) { - Internal def = (Internal)definition; - return getURI(resourceCount, identities, def.parent) + "/" + def.name; - } else { - return ""; - } - } - } - return ":"; - } + public static Value findValue(TransferableGraph1 tg, int subject) { + for(Value v : tg.values) { + if(v.resource == subject) return v; + } + return null; + } + + public static String getURI(TransferableGraph1 tg, int id) { + return getURI(tg.identities, id); + } + + public static String getURI(Identity[] identities, int id) { + for(Identity identity : identities) { + if(identity.resource == id) { + IdentityDefinition definition = identity.definition; + if(definition instanceof External) { + External def = (External)definition; + if(def.parent == -1) return "http:/"; + else return getURI(identities, def.parent) + "/" + def.name; + } else if(definition instanceof Root) { + Root def = (Root)definition; + if(def.name.isEmpty()) return "http:/"; + return def.name; + } else if (definition instanceof Internal) { + Internal def = (Internal)definition; + return getURI(identities, def.parent) + "/" + def.name; + } else { + return ""; + } + } + } + return ":"; + } - public static TIntObjectMap mapIdentities(TransferableGraph1 tg) { - return mapIdentities(tg.identities); - } + public static TIntObjectMap mapIdentities(TransferableGraph1 tg) { + return mapIdentities(tg.identities); + } - public static TIntObjectMap mapIdentities(Identity[] identities) { - // Integer.MIN_VALUE cannot be the value of Identity.resource - TIntObjectMap map = new TIntObjectHashMap<>(identities.length, 0.5f, Integer.MIN_VALUE); - for (Identity id : identities) - map.put(id.resource, id); - return map; - } + public static TIntObjectMap mapIdentities(Identity[] identities) { + // Integer.MIN_VALUE cannot be the value of Identity.resource + TIntObjectMap map = new TIntObjectHashMap<>(identities.length, 0.5f, Integer.MIN_VALUE); + for (Identity id : identities) + map.put(id.resource, id); + return map; + } - public static String getURI(int resourceCount, TIntObjectMap identities, int id) { - Identity identity = identities.get(id); - if(identity != null) { - IdentityDefinition definition = identity.definition; - if(definition instanceof External) { - External def = (External)definition; - if(def.parent == -1) return "http:/"; - else return getURI(resourceCount, identities, def.parent) + "/" + URIStringUtils.escape(def.name); - } else if(definition instanceof Root) { - Root def = (Root)definition; - if(def.name.isEmpty()) return "http:/"; - return def.name; - } else if (definition instanceof Internal) { - Internal def = (Internal)definition; - return getURI(resourceCount, identities, def.parent) + "/" + URIStringUtils.escape(def.name); - } else { - return ""; - } - } - return ":"; - } + public static String getURI(int resourceCount, TIntObjectMap identities, int id) { + Identity identity = identities.get(id); + if(identity != null) { + IdentityDefinition definition = identity.definition; + if(definition instanceof External) { + External def = (External)definition; + if(def.parent == -1) return "http:/"; + else return getURI(resourceCount, identities, def.parent) + "/" + URIStringUtils.escape(def.name); + } else if(definition instanceof Root) { + Root def = (Root)definition; + if(def.name.isEmpty()) return "http:/"; + return def.name; + } else if (definition instanceof Internal) { + Internal def = (Internal)definition; + return getURI(resourceCount, identities, def.parent) + "/" + URIStringUtils.escape(def.name); + } else { + return ""; + } + } + return ":"; + } } -- 2.43.2