import java.io.DataInput;
import java.io.DataInputStream;
import java.io.InputStream;
+import java.math.BigInteger;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
import java.util.TreeMap;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+import org.simantics.databoard.Bindings;
import org.simantics.databoard.binding.Binding;
+import org.simantics.databoard.binding.mutable.Variant;
import org.simantics.databoard.container.DataContainers;
+import org.simantics.databoard.parser.DataValuePrinter;
+import org.simantics.databoard.parser.PrintFormat;
+import org.simantics.databoard.parser.repository.DataValueRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import gnu.trove.list.array.TIntArrayList;
+import gnu.trove.map.hash.THashMap;
+import gnu.trove.map.hash.TIntIntHashMap;
import gnu.trove.map.hash.TIntObjectHashMap;
+import gnu.trove.procedure.TIntIntProcedure;
import gnu.trove.set.hash.TLongHashSet;
/**
* @author Antti Villberg
* @since 1.24.0
*/
-public class PrettyPrintTG extends TransferableGraphUtils {
-
- int blankCounter = 0;
-
- StringBuilder output = new StringBuilder();
-
- static class ResourceInfo {
- final boolean hasURI;
- final String name;
- final int resource;
- boolean newResource = false;
- int owner = 0;
- int ownerPredicate = 0;
- TIntArrayList owned = new TIntArrayList();
- TIntArrayList statements = new TIntArrayList();
- public ResourceInfo(boolean hasURI, String name, int resource) {
- this.hasURI = hasURI;
- this.name = name;
- this.resource = resource;
- }
- }
-
- TIntObjectHashMap<ResourceInfo> infos = new TIntObjectHashMap<>();
-
- ResourceInfo recurseURI(TransferableGraph1 graph, Identity parent, String parentName) {
- String name = parentName + ".\"" + getName(parent) + "\"";
- ResourceInfo info = new ResourceInfo(true, name, parent.resource);
- infos.put(parent.resource, info);
- for(Identity child : getChildren(graph, parent)) {
- recurseURI(graph, child, name);
- }
- return info;
- }
-
- void discoverBlank(TransferableGraph1 graph, int resource, TIntArrayList todo) {
- TIntArrayList statements = getStatements(graph, resource);
- for(int i=0;i<statements.size();i+=2) {
- int object = statements.get(i+1);
- Identity objectId = getIdentity(graph, object);
- if(objectId != null) {
- if(objectId.definition instanceof External) continue;
- }
- ResourceInfo existing = infos.get(object);
- if(existing == null) {
- existing = new ResourceInfo(false, "blank" + blankCounter++, object);
- infos.put(object, existing);
- todo.add(object);
- }
- }
- }
-
- void discoverOwners(TransferableGraph1 graph, ResourceInfo info) {
- int resource = info.resource;
- TIntArrayList statements = getStatements(graph, resource);
- for(int i=0;i<statements.size();i+=2) {
- int predicate = statements.get(i);
- int object = statements.get(i+1);
- ResourceInfo existing = infos.get(object);
- if(existing == null) continue;
- if(existing.owner == 0) {
- existing.owner = resource;
- existing.ownerPredicate = predicate;
- //System.err.println("First owner " + info.name + " => " + predicateURI + " " + existing.name);
- } else {
- existing.owner = -1;
- //System.err.println("Multiple owners " + info.name + " => " + predicateURI + " " + existing.name);
- }
- }
- info.statements = statements;
- }
-
- void fixInstanceOf(TransferableGraph1 graph, ResourceInfo info) {
- Identity id = getIdentity(graph, info.resource);
- if(id == null) return;
- if(id.definition instanceof Internal) {
- Identity instanceOf = findExternal(graph, "http://www.simantics.org/Layer0-1.1/InstanceOf");
- Identity library = findExternal(graph, "http://www.simantics.org/Layer0-1.1/Library");
- info.statements.add(instanceOf.resource);
- info.statements.add(library.resource);
- }
- }
-
- public static String getExternalURI(TransferableGraph1 tg, External ext) {
- String name = ext.name;
- if(name.contains(" ")) name = name.replace(" ", "_").replaceAll("@", "_");//name = "\"" + name + "\"";
- int parentId = ext.parent;
- if(parentId == 0) return ext.name;
- else {
- Identity id = getIdentity(tg, parentId);
- if(id.definition instanceof External) {
- return getExternalURI(tg, (External)id.definition) + "/" + name;
- } else if(id.definition instanceof Root) {
- Root root = (Root)id.definition;
- return "http:/" + root.name + "/" + name;
- } else {
- return null;
- }
- }
- }
-
- public static String getExternalURI(TransferableGraph1 tg, int resource) {
- Identity id = getIdentity(tg, resource);
- if(id == null) return null;
- if(id.definition instanceof External) {
- External ext = (External)id.definition;
- return getExternalURI(tg, ext);
- }
- return null;
- }
-
- String rewritePredicateURI(TransferableGraph1 graph, int predicate) {
- String uri = getExternalURI(graph, predicate);
- if(uri == null) return null;
- uri = uri.replace("http://www.simantics.org/Modeling-1.2", "MOD");
- uri = uri.replace("http://www.simantics.org/Layer0-1.1", "L0");
- uri = uri.replace("http://www.simantics.org/Layer0X-1.1", "L0X");
- uri = uri.replace("http://www.simantics.org/Diagram-2.2", "DIA");
- uri = uri.replace("http://www.simantics.org/Structural-1.2", "STR");
- uri = uri.replace("http://www.simantics.org/Documentation-1.2", "DOCU");
- uri = uri.replace("http://www.simantics.org/Document-1.2", "DOC");
- uri = uri.replace("http://www.simantics.org/G2D-1.1", "G2D");
- uri = uri.replace("http://www.simantics.org/Image2-1.2", "IMAGE2");
- uri = uri.replace("http://www.simantics.org/SelectionView-1.2", "SEL");
- uri = uri.replace("http://www.simantics.org/GraphFile-0.1", "GRAPHFILE");
- uri = uri.replace("http://www.semantum.fi/Simupedia-1.0", "SIMUPEDIA");
- uri = uri.replace("http://www.semantum.fi/SimupediaWorkbench-1.0", "SIMUPEDIA_WB");
- uri = uri.replace("http://www.apros.fi/OperationUI-6.6", "APROS_OPER");
- uri = uri.replace("http://semantum.fi/SimupediaStandardLibrary@1.3-trunk", "SIMUPEDIA_STD");
- uri = uri.replace("/", ".");
- return uri;
- }
-
- void printBlank(TransferableGraph1 graph, String predicateURI2, ResourceInfo info) {
-
- if(info.hasURI) return;
- output.append(" " + predicateURI2 + " " + info.name + "\n");
-
- Value value = findValue(graph, info.resource);
- if(value != null) {
-
- }
-
-// for(int i=0;i<info.owned.size();i+=2) {
-// String predicateURI = rewritePredicateURI(graph, info.owned.get(i));
-// ResourceInfo ownedInfo = infos.get(info.owned.get(i+1));
-// if(ownedInfo == null) {
-// System.err.println("null owned");
-// continue;
-// }
-// printBlank(graph, predicateURI, ownedInfo);
-// }
-
- }
-
- long longStm(int predicate, int object) {
- return (predicate<<32) | (object & 0xffffffffL);
- }
-
- void printURI(TransferableGraph1 graph, ResourceInfo info) {
- if(!info.hasURI) return;
- if("ROOT".equals(info.name)) {
- output.append("ROOT=<http:/>\n");
- } else {
- output.append(info.name + "\n");
- }
- if(info.newResource)
- output.append(" @L0.new\n");
- TLongHashSet processed = new TLongHashSet();
- for(int i=0;i<info.owned.size();i+=2) {
- String predicateURI = rewritePredicateURI(graph, info.owned.get(i));
- ResourceInfo ownedInfo = infos.get(info.owned.get(i+1));
- if(ownedInfo == null) {
- System.err.println("null owned");
- continue;
- }
- long stmId = longStm(info.owned.get(i), info.owned.get(i+1));
- processed.add(stmId);
- printBlank(graph, predicateURI, ownedInfo);
- }
- Identity consistsOf = findExternal(graph, "http://www.simantics.org/Layer0-1.1/ConsistsOf");
- for(int i=0;i<info.statements.size();i+=2) {
- long stmId = longStm(info.statements.get(i), info.statements.get(i+1));
- if(processed.contains(stmId)) continue;
- if(consistsOf.resource == info.statements.get(i)) continue;
- String predicateURI = rewritePredicateURI(graph, info.statements.get(i));
- ResourceInfo objectInfo = infos.get(info.statements.get(i+1));
- if(objectInfo == null) {
- String objectURI = rewritePredicateURI(graph, info.statements.get(i+1));
- output.append(" " + predicateURI + " " + objectURI + "\n");
- } else {
- output.append(" " + predicateURI + " " + objectInfo.name + "\n");
- }
- }
- }
-
- 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);
- // Discover resources with URI
- for(Identity id : TransferableGraphUtils.getRoots(graph)) {
- String name = "ROOT";
- ResourceInfo info = new ResourceInfo(true, name, id.resource);
- infos.put(id.resource, info);
- for(Identity child : getChildren(graph, id)) {
- ResourceInfo childInfo = recurseURI(graph, child, name);
- childInfo.newResource = true;
- }
- }
- // Discover other resources
- TIntArrayList todo = new TIntArrayList();
- for(ResourceInfo info : infos.valueCollection())
- todo.add(info.resource);
- while(!todo.isEmpty()) {
- int resource = todo.removeAt(todo.size()-1);
- discoverBlank(graph, resource, todo);
- }
- for(ResourceInfo info : infos.valueCollection())
- discoverOwners(graph, info);
- for(ResourceInfo info : infos.valueCollection())
- fixInstanceOf(graph, info);
- for(ResourceInfo info : infos.valueCollection())
- if(info.owner > 0) {
- ResourceInfo ownerInfo = infos.get(info.owner);
- ownerInfo.owned.add(info.ownerPredicate);
- ownerInfo.owned.add(info.resource);
- } else if (info.owner == 0) {
- //System.err.println("faf1");
- } else if (info.owner == -1) {
- //System.err.println("faf2");
- }
-
- TreeMap<String,ResourceInfo> order = new TreeMap<>();
- for(ResourceInfo info : infos.valueCollection())
- order.put(info.name, info);
-
- this.output.append("MOD = <http://www.simantics.org/Modeling-1.2>\n");
- this.output.append("L0 = <http://www.simantics.org/Layer0-1.1>\n");
- this.output.append("L0X = <http://www.simantics.org/Layer0X-1.1>\n");
- this.output.append("DIA = <http://www.simantics.org/Diagram-2.2>\n");
- this.output.append("STR = <http://www.simantics.org/Structural-1.2>\n");
- this.output.append("DOCU = <http://www.simantics.org/Documentation-1.2>\n");
- this.output.append("DOC = <http://www.simantics.org/Document-1.2>\n");
- this.output.append("G2D = <http://www.simantics.org/G2D-1.1>\n");
- this.output.append("SEL = <http://www.simantics.org/SelectionView-1.2>\n");
- this.output.append("IMAGE2 = <http://www.simantics.org/Image2-1.2>\n");
- this.output.append("GRAPHFILE = <http://www.simantics.org/GraphFile-0.1>\n");
- this.output.append("APROS_OPER = <http://www.apros.fi/OperationUI-6.6>\n");
- this.output.append("SIMUPEDIA = <http://www.semantum.fi/Simupedia-1.0>\n");
- this.output.append("SIMUPEDIA_WB = <http://www.semantum.fi/SimupediaWorkbench-1.0>\n");
- this.output.append("SIMUPEDIA_STD = <http://semantum.fi/SimupediaStandardLibrary@1.3-trunk>\n");
-
-// uri = uri.replace("http://semantum.fi/SimupediaStandardLibrary@1.3-trunk/", "SIMUPEDIA_STD.");
-
-
- for(ResourceInfo info : order.values())
- printURI(graph, info);
-
- Files.write(output, this.output.toString().getBytes());
-
- }
- }
-
- public static void main(String[] args) throws Exception {
- if (args.length < 1) {
- System.out.println("Required arguments: <input .sharedOntology file> [<output .tg file>]");
- } 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);
- } else {
- new PrettyPrintTG().prettyPrint(Paths.get(args[0]), Paths.get(args[1]));
- }
- }
+public class PrettyPrintTG {
+
+ private static final Logger LOGGER = LoggerFactory.getLogger(PrettyPrintTG.class);
+
+ private static final boolean DEBUG = false;
+
+ int blankCounter = 0;
+ int newBlankCounter = 0;
+ Map<String, String> blankRewrites = new HashMap<>();
+ MessageDigest m;
+
+ private final Pattern versionExtractPattern = Pattern.compile("^.*-(\\d+\\.\\d+)");
+
+ final StringBuilder output;
+ final Map<String, String> ontologies = new HashMap<>(knownOntologies);
+ final Set<String> referencedOntologies = new TreeSet<>();
+
+ private boolean ignoreIdentifiers;
+
+ private TransferableGraphQueries query;
+
+ static class ResourceInfo {
+ final boolean hasURI;
+ String name;
+ final int resource;
+ boolean newResource = false;
+
+ int parent;
+
+ boolean inlined = false;
+
+ // -1 = no owner, -2 = multiple owners
+
+ // Set<ResourceInfo> ownedBy
+ Set<ResourceInfo> ownedBy = new HashSet<>();
+
+ // A Map<Integer, Integer> containing information about resource that
+ // this resource owns and what are the predicates for forming this
+ // ownership
+ TIntIntHashMap ownedResourcesWithPredicates = new TIntIntHashMap();
+
+ // int owner = -1;
+ // int ownerPredicate = 0;
+ String aliasURI = null;
+ TIntArrayList owned = new TIntArrayList();
+
+ // TIntObjectHashMap<TIntHashSet> statements = new
+ // TIntObjectHashMap<TIntHashSet>();
+ public ResourceInfo(boolean hasURI, String name, int resource, int parent) {
+ this.hasURI = hasURI;
+ this.name = name;
+ this.resource = resource;
+ this.parent = parent;
+ }
+
+ @Override
+ public String toString() {
+ return name + (aliasURI != null ? " = <" + aliasURI + ">" : "");
+ }
+ }
+
+ 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(TransferableGraph1 tg) throws NoSuchAlgorithmException {
+ this(tg, new StringBuilder(), false);
+ }
+
+ TreeMap<String, ResourceInfo> orderedInfos = new TreeMap<>();
+ TIntObjectHashMap<ResourceInfo> infos = new TIntObjectHashMap<>();
+
+ private static String tgNodeName(String name) {
+ if (name.contains(" "))
+ return "\"" + name + "\"";
+ else
+ return name;
+ }
+
+ private ResourceInfo recurseURI(Map<String, ResourceInfo> 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;
+ }
+
+ /**
+ * Sorts statements by predicateURI in natural order
+ *
+ * @param graph
+ * @param resource
+ * @return
+ */
+ private TreeMap<String, TreeSet<Integer>> sortByPredicateUniqueStatements(int resource) {
+ TreeMap<String, TreeSet<Integer>> results = new TreeMap<>();
+ TIntArrayList statements = query.getStatements(resource);
+ for (int i = 0; i < statements.size(); i += 2) {
+ int predicate = statements.get(i);
+ String predicateURI = query.getURI(predicate);
+ TreeSet<Integer> objects = results.get(predicateURI);
+ if (objects == null) {
+ objects = new TreeSet<>();
+ }
+ objects.add(statements.get(i + 1));
+ results.put(predicateURI, objects);
+ }
+ return results;
+ }
+
+ void discoverBlank(int resource, TIntArrayList todo) throws Exception {
+ // TIntArrayList statements =
+ // TransferableGraphUtils.getStatements(graph, resource);
+ // for(int i=0;i<statements.size();i+=2) {
+ for (TreeSet<Integer> objects : sortByPredicateUniqueStatements(resource).values()) {
+ for (int object : objects) {
+ // int object = statements.get(i+1);
+ Identity objectId = query.getIdentity(object);
+ if (objectId != null) {
+ if (objectId.definition instanceof External)
+ continue;
+ }
+ Value value = query.findValue(object);
+ if (value != null) {
+ infos.put(object, new ResourceInfo(false, printValue(value), object, resource));
+ } 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);
+ }
+ }
+ }
+ }
+ }
+
+ private String makeHash(byte[] data) {
+ m.reset();
+ m.update(data, 0, data.length);
+ return new BigInteger(1, m.digest()).toString(16);
+ }
+
+ void discoverOwners(ResourceInfo info) {
+ log("Discovering owners for {}", info);
+ int resource = info.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);
+ ResourceInfo existing = infos.get(object);
+ if (existing != null) {
+ // Add all owners here for now and resolve the best owner later
+
+ // Check if predicate is inverse, this just resolves all
+ // predicates to be inverse with ending "Inverse"..
+ String predicateUri = rewritePredicateURI(predicate);
+ if (!predicateUri.endsWith("Inverse") && !predicateUri.endsWith("Of")) {
+ existing.ownedResourcesWithPredicates.put(resource, predicate);
+ // if (predicateUri.endsWith("Of")) {
+ // System.out.println("asd");
+ // } else {
+ existing.ownedBy.add(info);
+ log(" {} owns {} with {}", existing, info, predicateUri);
+ // }
+ } else {
+ // System.out.println("asd");
+ }
+ }
+ }
+ }
+
+ DataValueRepository repo = new DataValueRepository();
+ DataValuePrinter printer = new DataValuePrinter(null, repo);
+
+ String printValue(Value value) throws Exception {
+ StringBuilder sb = new StringBuilder();
+ printer.setFormat(PrintFormat.SINGLE_LINE);
+ printer.setOutput(sb);
+
+ Variant variant = value.value;
+ printer.print(variant.getBinding(), variant.getValue());
+ String formattedOutput = sb.toString();
+ if (formattedOutput.length() > 100) {
+ // Ok, value too long, lets calculate a hash for it and store first
+ // 100 chars as comment
+ byte[] data = Bindings.getSerializerUnchecked(variant.getBinding()).serialize(variant.getValue());
+ m.reset();
+ m.update(data, 0, data.length);
+ String hash = "\"" + new BigInteger(1, m.digest()).toString(16) + "\"";
+ return hash + " // " + formattedOutput.substring(0, 100) + "..";
+ } else {
+ return formattedOutput;
+ }
+ }
+
+ public String getExternalURI(External ext) {
+ String name = ext.name;
+ if (name.contains(" "))
+ name = name.replace(" ", "_").replaceAll("@", "_");// name = "\"" +
+ // name + "\"";
+ int parentId = ext.parent;
+ // if(parentId == 0) return ext.name;
+ // else {
+ Identity id = query.getIdentity(parentId);
+ if (id.definition instanceof External) {
+ return getExternalURI((External) id.definition) + "/" + name;
+ } else if (id.definition instanceof Root) {
+ Root root = (Root) id.definition;
+ return "http:/" + root.name + "/" + name;
+ } else {
+ return null;
+ }
+ // }
+ }
+
+ 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(ext);
+ }
+ return null;
+ }
+
+ String rewritePredicateURI(int predicate) {
+
+ String uri = getExternalURI(predicate);
+ if (uri == null) {
+ ResourceInfo info = infos.get(predicate);
+ if (info != null)
+ return info.name;
+ return "_";
+ }
+
+ for (String ontology : ontologies.keySet()) {
+ if (uri.contains(ontology)) {
+ String key = ontologies.get(ontology);
+ uri = uri.replace(ontology, key);
+ referencedOntologies.add(ontology);
+ }
+ }
+
+ uri = uri.replace("/", ".");
+
+ return uri;
+
+ }
+
+ static void indent(StringBuilder output, int indent) {
+ for (int i = 0; i < indent; i++)
+ output.append(" ");
+ }
+
+ String printBlank(String predicateURI2, ResourceInfo info, int indent) {
+
+ if (info.hasURI)
+ return null;
+
+ StringBuilder output = new StringBuilder();
+
+ String infoName = info.name;
+ if (infoName.startsWith("blank")) {
+ infoName = getBlankRewrite(infoName);
+ }
+
+ if (ignoreIdentifiers) {
+ if (predicateURI2.contains("L0.identifier")) {
+ // Do nothing
+ } else {
+ indent(output, indent);
+ output.append(predicateURI2 + " " + infoName + "\n");
+ }
+ } else {
+ indent(output, indent);
+ output.append(predicateURI2 + " " + infoName + "\n");
+ }
+
+ if (info.ownedResourcesWithPredicates.isEmpty()) {
+ if (DEBUG)
+ System.out.print("printBlank");
+ String uri = printURI(info, false, indent, false);
+ if (uri != null)
+ output.append(uri);
+ }
+ // if(info.owner < 0) {
+ // printURI(graph, info, false, indent);
+ // }
+ return output.toString();
+ }
+
+ private String getBlankRewrite(String infoName) {
+ String rewrite = blankRewrites.get(infoName);
+ if (rewrite == null) {
+ rewrite = "rblank" + newBlankCounter++;
+ if (DEBUG)
+ System.out.println("rewrote " + infoName + " to " + rewrite);
+ blankRewrites.put(infoName, rewrite);
+ }
+ return rewrite;
+ // return infoName;
+ }
+
+ static long longStm(int predicate, int object) {
+ return ((predicate & 0xffffffffL) << 32) | (object & 0xffffffffL);
+ }
+
+ private void addInlineStatement(Map<String, Set<String>> statements, String predicate,
+ ResourceInfo objectInfo, int indent) {
+ Set<String> objects = statements.get(predicate);
+ if (objects == null) {
+ objects = new TreeSet<>();
+ statements.put(predicate, objects);
+ }
+ 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;
+ objects.add(uri);
+ }
+ objectInfo.inlined = true;
+ }
+
+ void addStatement(Map<String, Set<String>> statements, String predicate, String object) {
+ // TODO: fix this
+ if (predicate.endsWith("Inverse"))
+ return;
+ Set<String> objects = statements.get(predicate);
+ if (objects == null) {
+ objects = new TreeSet<>();
+ statements.put(predicate, objects);
+ }
+ objects.add(object);
+ }
+
+ String printURI(ResourceInfo info, boolean requireURI, int indent, boolean inline) {
+
+ if (requireURI && !info.hasURI)
+ return null;
+
+ // Check if this ResourceInfo is already inlined with some other
+ // ResourceInfo
+ if (info.inlined)
+ return null;
+
+ Map<String, Set<String>> statements = new TreeMap<>();
+ 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();
+ if (DEBUG)
+ System.out.println("info.owned.size " + info.owned.size() + info.owned);
+ for (int i = 0; i < info.owned.size(); i += 2) {
+ int predicate = info.owned.get(i);
+ int object = info.owned.get(i + 1);
+ long stmId = longStm(predicate, object);
+ if (DEBUG)
+ System.out.println(
+ " " + stmId + " is already processed as it is owned (" + predicate + " " + object + ")");
+ processed.add(stmId);
+ }
+
+ TreeMap<String, List<Integer>> predicateURIs = new TreeMap<>();
+
+ TIntArrayList rawStatements = query.getStatements(info.resource);
+ if (DEBUG)
+ System.out.println(
+ "rawStatements size for " + info.name + " : " + rawStatements.size() + " " + rawStatements);
+ for (int i = 0; i < rawStatements.size(); i += 2) {
+ int predicate = rawStatements.get(i);
+ int object = rawStatements.get(i + 1);
+ long stmId = longStm(predicate, object);
+ if (!processed.add(stmId)) {
+ if (DEBUG)
+ System.out.println(" " + stmId + " is already processed (" + (predicate & 0xffffffffL) + " "
+ + (object & 0xffffffffL) + ")");
+ continue;
+ }
+ if (DEBUG)
+ System.out.println(" " + stmId + " is currently being processed (" + (predicate & 0xffffffffL) + " "
+ + (object & 0xffffffffL) + ")");
+ // if (partOf.resource == rawStatements.get(i))
+ // continue;
+ if (consistsOf.resource == predicate) {
+ // if (!info.owned.isEmpty() && !info.name.startsWith("blank"))
+ // {
+ if (DEBUG)
+ System.out.println(" is consistsof " + predicate + " (" + consistsOf.resource + ")");
+ continue;
+ // } else {
+ // // this will be inlined so lets indent
+ // indent++;
+ // }
+ }
+ String predicateURI = rewritePredicateURI(predicate);
+ List<Integer> objects = predicateURIs.get(predicateURI);
+ if (objects == null) {
+ objects = new ArrayList<>();
+ predicateURIs.put(predicateURI, objects);
+ }
+ objects.add(object);
+ }
+ for (Entry<String, List<Integer>> entry : predicateURIs.entrySet()) {
+ String predicateURI = entry.getKey();
+ List<Integer> 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(
+ "statements size for " + info.name + " : " + statements.size() + " " + statements.keySet());
+
+ StringBuilder output = new StringBuilder();
+
+ if (indent == 0 || inline) {
+ if ("ROOT".equals(info.name)) {
+ output.append("ROOT=<http:/>");
+ } else if (info.aliasURI != null) {
+ output.append(info.name + " = <" + info.aliasURI + ">");
+ } else {
+ String infoName = info.name;
+ if (infoName.startsWith("blank")) {
+ infoName = getBlankRewrite(infoName);
+ }
+ output.append(inline ? "_" : infoName);
+ }
+ Set<String> instanceOfs = statements.get("L0.InstanceOf");
+ if (instanceOfs != null) {
+ for (String instanceOf : instanceOfs) {
+ output.append(" : " + instanceOf);
+ }
+ }
+ Set<String> subrelationOfs = statements.get("L0.SubrelationOf");
+ if (subrelationOfs != null) {
+ for (String subrelationOf : subrelationOfs) {
+ output.append(" <R " + subrelationOf);
+ }
+ }
+ Set<String> inherits = statements.get("L0.Inherits");
+ if (inherits != null) {
+ for (String inherit : inherits) {
+ output.append(" <T " + inherit);
+ }
+ }
+ output.append("\n");
+ }
+
+ if (info.newResource)
+ output.append(" @L0.new\n");
+
+ for (Map.Entry<String, Set<String>> entry : statements.entrySet()) {
+ String predicate = entry.getKey();
+ if (ignoreIdentifiers) {
+ if (predicate.equals("L0.identifier")) {
+ continue;
+ }
+ }
+ if ("L0.InstanceOf".equals(predicate))
+ continue;
+ if ("L0.SubrelationOf".equals(predicate))
+ continue;
+ if ("L0.Inherits".equals(predicate))
+ continue;
+ if ("L0.PartOf".equals(predicate))
+ continue;
+
+ // predicates can be blank
+ if (predicate.startsWith("blan")) {
+ predicate = getBlankRewrite(predicate);
+ }
+
+ Set<String> objects = entry.getValue();
+ indent(output, indent + 1);
+ if (objects.size() == 1) {
+ output.append(predicate + " " + objects.iterator().next() + "\n");
+ } else {
+ output.append(predicate + "\n");
+ for (String object : objects) {
+ indent(output, indent + 1);
+ output.append(" " + object + "\n");
+ }
+ }
+ }
+
+ TreeMap<String, Set<Integer>> ownedOrdered = new TreeMap<>();
+
+ for (int i = 0; i < info.owned.size(); i += 2) {
+ String predicateURI = rewritePredicateURI(info.owned.get(i));
+ Set<Integer> 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<String, Set<Integer>> entry : ownedOrdered.entrySet()) {
+ String predicateURI = entry.getKey();
+ Set<Integer> 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();
+ }
+
+ static Map<String, String> knownOntologies = new HashMap<>();
+
+ static {
+ knownOntologies.put("http://www.simantics.org/Layer0-1.1", "L0");
+ knownOntologies.put("http://www.simantics.org/Layer0X-1.1", "L0X");
+ knownOntologies.put("http://www.simantics.org/Modeling-1.2", "MOD");
+ knownOntologies.put("http://www.simantics.org/Diagram-2.2", "DIA");
+ knownOntologies.put("http://www.simantics.org/Structural-1.2", "STR");
+ knownOntologies.put("http://www.simantics.org/Document-1.2", "DOC");
+ knownOntologies.put("http://www.simantics.org/Documentation-1.2", "DOCU");
+ knownOntologies.put("http://www.simantics.org/G2D-1.1", "G2D");
+ knownOntologies.put("http://www.simantics.org/SelectionView-1.2", "SEL");
+ knownOntologies.put("http://www.simantics.org/Viewpoint-1.2", "VP");
+ knownOntologies.put("http://www.simantics.org/Image2-1.2", "IMAGE2");
+ knownOntologies.put("http://www.simantics.org/GraphFile-0.1", "GRAPHFILE");
+ knownOntologies.put("http://www.simantics.org/Project-1.2", "PROJECT");
+ knownOntologies.put("http://www.semantum.fi/Simupedia-1.0", "SIMUPEDIA");
+ knownOntologies.put("http://www.semantum.fi/SimupediaWorkbench-1.0", "SIMUPEDIA_WORKBENCH");
+ }
+
+ void prettyPrint() throws Exception {
+ log("Starting prettyPrint for TransferableGraph with {} resources, {} identities, {} statements and {} values",
+ query.getGraph().resourceCount, query.getGraph().identities, query.getGraph().statements.length, query.getGraph().values.length);
+
+ query.forIdentities(id -> {
+ int identityResource = id.resource;
+ if (id.definition instanceof Internal) {
+ Internal internal = (Internal) id.definition;
+ 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, 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 : query.getChildren(id))
+ recurseURI(orderedInfos, child, name, identityResource);
+ log(" and has {} children", infos.size());
+ }
+ } else if (id.definition instanceof External) {
+ External ext = (External) id.definition;
+ // Try to detect shared libraries
+ if (ext.name.contains("@")) {
+
+ log("Detected an external shared library {}", ext);
+
+ int index = ext.name.indexOf('@');
+ 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 = query.getURI(identityResource);
+
+ log(" which was resolved as URI={} and prefix={}", uri, prefix);
+
+ ontologies.put(uri, prefix);
+
+ } else if (ext.name.contains("-")) {
+ log("Resolving possible ontology {}", ext);
+ String uri = query.getURI(identityResource);
+ Matcher m = versionExtractPattern.matcher(uri);
+ if (m.matches()) {
+ if (!ontologies.containsKey(uri)) {
+ int index = ext.name.indexOf('-');
+ String prefix = ext.name.substring(0, index);
+ log(" and it was resolved as URI={} and prefix {}", uri, prefix);
+ ontologies.put(uri, prefix);
+ }
+ }
+ }
+ }
+ return true;
+ });
+
+ // Discover other resources
+ log("Discovering other resources..");
+
+ TIntArrayList todo = new TIntArrayList();
+ for (ResourceInfo info : orderedInfos.values()) {
+ todo.add(info.resource);
+
+ // put orderedInfos to infos
+ infos.put(info.resource, info);
+ }
+
+ while (!todo.isEmpty()) {
+ int resource = todo.removeAt(todo.size() - 1);
+ discoverBlank(resource, todo);
+ }
+ for (ResourceInfo info : infos.valueCollection())
+ discoverOwners(info);
+ // for(ResourceInfo info : infos.valueCollection())
+ // fixInstanceOf(graph, info);
+
+ for (ResourceInfo info : infos.valueCollection()) {
+ // Old implementation
+ // if (info.owner >= 0) {
+ // ResourceInfo ownerInfo = infos.get(info.owner);
+ // System.out.println("originalOwner : " + info.owner + "
+ // originalPredicate: " + info.ownerPredicate);
+ // ownerInfo.owned.add(info.ownerPredicate);
+ // ownerInfo.owned.add(info.resource);
+ // }
+
+ if (!info.ownedResourcesWithPredicates.isEmpty() && info.ownedResourcesWithPredicates.size() == 1) {
+ info.ownedResourcesWithPredicates.forEachEntry(new TIntIntProcedure() {
+
+ @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);
+ }
+ }
+
+ // Resolve inverses from ownedBy list
+ for (ResourceInfo info : infos.valueCollection()) {
+ for (int i = 0; i < info.owned.size(); i += 2) {
+ int object = info.owned.get(i + 1);
+ ResourceInfo inf = infos.get(object);
+ if (inf != null) {
+ info.ownedBy.remove(inf);
+ }
+ }
+ }
+
+ 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()) {
+ if (elemTo != null) {
+ int elemToComponent = query.getPossibleObject(infoo.resource, elemTo);
+ if (elemToComponent != TransferableGraphUtils.NOT_FOUND) {
+
+ 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;
+ }
+ }
+ }
+
+ if (instanceOf != null) {
+ 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 = query.getPossibleObject( infoo.resource,
+ diagramConnetionToConnection);
+ if (connection != TransferableGraphUtils.NOT_FOUND) {
+ // Gather all inverse statements to construct unique
+ // name
+ List<String> nameParts = new ArrayList<>();
+ TIntArrayList statements = query.getStatements(connection);
+ for (int i = 0; i < statements.size(); i += 2) {
+ int predicate = statements.get(i);
+ 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 = query.getPossibleObject(
+ connection, possibleInverse);
+ parentId = iPossibleInverse.parent;
+ } else {
+ log("Unsupported inverse relation found for {} {}", infoo, iPossibleInverse);
+ }
+ } else if (possibleInverse.definition instanceof External) {
+ External ePossibleInverse = (External) possibleInverse.definition;
+ if (ePossibleInverse.name.equals("Inverse")) {
+ inverseRelation = query.getPossibleObject(
+ connection, possibleInverse);
+ parentId = ePossibleInverse.parent;
+ } else {
+ log("This external inverse is unsupported for {} {}", infoo, ePossibleInverse);
+ }
+ } else {
+ log("This type of definition is not supported {}", infoo);
+ }
+ if (inverseRelation != TransferableGraphUtils.NOT_FOUND) {
+ // Ok found something
+ Identity object = query.getIdentity(inverseRelation);
+ Identity parent = query.getIdentity(parentId);
+ String objectName, parentName;
+ if (object.definition instanceof Internal) {
+ objectName = ((Internal) object.definition).name;
+ } else if (object.definition instanceof External) {
+ objectName = ((External) object.definition).name;
+ } else {
+ log("This type of definition is not supported {}", infoo);
+ throw new Error("UNSUPPORTED " + infoo);
+ }
+ if (parent.definition instanceof Internal) {
+ parentName = ((Internal) parent.definition).name;
+ } else if (parent.definition instanceof External) {
+ parentName = ((External) parent.definition).name;
+ } else {
+ log("This type of definition is not supported {}", infoo);
+ throw new Error("UNSUPPORTED " + infoo);
+ }
+ String fullName = parentName + "_" + objectName;
+ nameParts.add(fullName);
+ } else {
+ log("No inverse relation found for {}", infoo);
+ }
+ } else {
+ log("Did not find possible inverse relation for {}", infoo);
+ }
+ }
+ nameParts.sort((o1, o2) -> o1.compareTo(o2));
+ String name = "";
+ for (String namep : nameParts) {
+ name += namep;
+ }
+ 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("Subject -> Predicate : " + infoo.resource + " -> "
+ + diagramConnetionToConnection.resource);
+ }
+ }
+ }
+ }
+ }
+ for (ResourceInfo info : infos.valueCollection()) {
+ if (info.name.startsWith("blank")) {
+ info.name = "blank" + findHash(info);
+ }
+ }
+
+ TreeMap<String, ResourceInfo> order = new TreeMap<>();
+ for (ResourceInfo info : infos.valueCollection())
+ order.put(info.name, info);
+
+ for (ResourceInfo info : order.values()) {
+ if (DEBUG)
+ System.out.print("info ");
+ String uri = printURI(info, true, 0, false);
+ if (uri != null)
+ output.append(uri);
+ }
+
+ TreeMap<String, ResourceInfo> rblanks = new TreeMap<>();
+
+ for (ResourceInfo info : order.values()) {
+ if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) {
+ if (DEBUG)
+ System.out.print("ownedResources ");
+ if (info.name.startsWith("blank")) {
+ // These will be printed later
+ rblanks.put(getBlankRewrite(info.name), info);
+ } else {
+ String uri = printURI(info, false, 0, false);
+ if (uri != null)
+ output.append(uri);
+ }
+ }
+ }
+ // Now print blanks in order
+ for (ResourceInfo info : rblanks.values()) {
+ if (!info.hasURI && info.ownedResourcesWithPredicates.size() != 1) {
+ if (DEBUG)
+ System.out.print("ownedResources ");
+ String uri = printURI(info, false, 0, false);
+ if (uri != null)
+ output.append(uri);
+ }
+ }
+
+ // for(ResourceInfo info : order.values())
+ // if(!info.hasURI && info.owner < 0)
+ // printURI(graph, info, false, 0);
+
+ StringBuilder refs = new StringBuilder();
+ for (String ontology : referencedOntologies) {
+ String key = ontologies.get(ontology);
+ refs.append(key + " = <" + ontology + ">\n");
+ }
+ if (!referencedOntologies.isEmpty())
+ refs.append("\n");
+ output.insert(0, refs.toString());
+
+ }
+
+ private String calculateHash(ResourceInfo info) {
+ StringBuilder statementHash = new StringBuilder();
+ TreeSet<String> parts = new TreeSet<>();
+ for (int i = 0; i < info.owned.size(); i += 2) {
+ int predicate = info.owned.get(i);
+ int object = info.owned.get(i + 1);
+ // Lets resolve a unique name for this based on the statements this
+ // one has
+
+ String predicatee = rewritePredicateURI(predicate);
+ ResourceInfo objInfo = infos.get(object);
+ parts.add(predicatee + "->" + objInfo.name + ";;;");
+ }
+ // Remove this from the list
+ List<ResourceInfo> filtered = info.ownedBy.stream().filter(ri -> !ri.name.startsWith("blank"))
+ .collect(Collectors.toList());
+ for (ResourceInfo ownedBy : filtered) {
+ parts.add(ownedBy.name);
+ }
+ // check parent
+ ResourceInfo parentInfo = infos.get(info.parent);
+ if (parentInfo != null && !parentInfo.name.startsWith("blank")) {
+ parts.add("parent" + parentInfo.name);
+ } else {
+ // LOGGER.error("This should not happen");
+ }
+ for (String s : parts) {
+ statementHash.append(s);
+ }
+ String hash = makeHash(statementHash.toString().getBytes());
+ if (DEBUG)
+ System.out.println(statementHash + " -> " + hash);
+ return hash;
+ }
+
+ 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(info);
+ if (hashes.put(oldName, hash) != null) {
+ System.err.println("!!!!A clash occured for " + info + " with hash " + hash);
+ }
+ }
+ return hash;
+ } else {
+ return info.name;
+ }
+ }
+
+ private THashMap<String, String> hashes = new THashMap<>();
+
+ public static String print(TransferableGraph1 tg, boolean ignoreIdentifiers) throws Exception {
+ StringBuilder b = new StringBuilder();
+ 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: <input .sharedOntology file> [<output .tg file>]");
+ }
+ Path input;
+ Path output;
+ if (args.length < 2) {
+ input = Paths.get(args[0]);
+ output = input.getParent().resolve(input.getName(input.getNameCount() - 1) + ".fixed");
+ } else {
+ 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();
+ }
+ }
+
+ private static void log(String string, Object... args) {
+ if (LOGGER.isDebugEnabled() && DEBUG)
+ LOGGER.debug(string, args);
+ }
}
Code Review / simantics / platform.git / blobdiff