package org.simantics.graph.representation;

import java.io.BufferedInputStream;
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.Arrays;
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 {

    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;

	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(StringBuilder b, boolean ignoreIdentifiers) throws NoSuchAlgorithmException {
		output = b;
		m = MessageDigest.getInstance("SHA-256");
		this.ignoreIdentifiers = ignoreIdentifiers;
	}

	public PrettyPrintTG() throws NoSuchAlgorithmException {
		this(new StringBuilder(), false);
	}

	TreeMap<String, ResourceInfo> orderedInfos = new TreeMap<>();
	TIntObjectHashMap<ResourceInfo> infos = new TIntObjectHashMap<>();

	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);
		}
		return info;
	}

    private TreeMap<String, TreeSet<Integer>> sortByPredicateUniqueStatements(TransferableGraph1 graph, int resource) {
        TreeMap<String, TreeSet<Integer>> results = new TreeMap<>();
        TIntArrayList statements = TransferableGraphUtils.getStatements(graph, resource);
        for (int i = 0; i < statements.size(); i += 2) {
            int predicate = statements.get(i);
            String predicateURI = TransferableGraphUtils.getURI(graph, 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(TransferableGraph1 graph, 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(graph, resource).values()) {
		    for (int object : objects) {
    //			int object = statements.get(i+1);
    			Identity objectId = TransferableGraphUtils.getIdentity(graph, object);
    			if(objectId != null) {
    				if(objectId.definition instanceof External) continue;
    			}
    			Value value = TransferableGraphUtils.findValue(graph, 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);
//                    existing = new ResourceInfo(false, "blank" + makeHash(statementHash.toString().getBytes()), object, resource);
    				
    				String resourceURI = TransferableGraphUtils.getURI(graph, resource);
    				String objectURI = TransferableGraphUtils.getURI(graph, object);
    				
    //				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(TransferableGraph1 graph, ResourceInfo info) {
	    log("Discovering owners for " + info);
		int resource = info.resource;
		TIntArrayList statements = TransferableGraphUtils.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) {
                // 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(graph, 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("    " + existing + " owns " + info + " with " + 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;
        }
//        
//        Variant variant = value.value;
//        Datatype dt = variant.getBinding().type();
//        if (Datatypes.STRING.equals(dt)) {
//            String s = (String) variant.getValue(Bindings.STRING);
//            if (s.contains("\n")) {
//                return "\"\"\"" + s + "\"\"\"";
//            } else {
//                return "\"" + s + "\"";
//            }
//        } else if (Datatypes.BOOLEAN.equals(dt)) {
//            Boolean i = (Boolean) variant.getValue(Bindings.BOOLEAN);
//            return i ? "true" : "false";
//        } else if (Datatypes.INTEGER.equals(dt)) {
//            Integer i = (Integer) variant.getValue(Bindings.INTEGER);
//            return i.toString();
//        } else if (Datatypes.LONG.equals(dt)) {
//            Long i = (Long) variant.getValue(Bindings.LONG);
//            return i.toString();
//        } else if (Datatypes.DOUBLE.equals(dt)) {
//            Double d = (Double) variant.getValue();
//            return d.toString();
//        } else if (Datatypes.FLOAT.equals(dt)) {
//            Float f = (Float) variant.getValue();
//            return f.toString();
//        } else if (Datatypes.STRING_ARRAY.equals(dt)) {
//            return Arrays.toString((String []) variant.getValue());
//        } else if (Datatypes.BOOLEAN_ARRAY.equals(dt)) {
//            return Arrays.toString((boolean []) variant.getValue());
//        } else if (Datatypes.INTEGER_ARRAY.equals(dt)) {
//            return Arrays.toString((int []) variant.getValue());
//        } else if (Datatypes.LONG_ARRAY.equals(dt)) {
//            return Arrays.toString((long []) variant.getValue());
//        } else if (Datatypes.DOUBLE_ARRAY.equals(dt)) {
//            return Arrays.toString((double []) variant.getValue());
//        } else if (Datatypes.FLOAT_ARRAY.equals(dt)) {
//            return Arrays.toString((float []) variant.getValue());
//        } else if (Datatypes.BYTE_ARRAY.equals(dt)) {
//            return Arrays.toString((byte []) variant.getValue());
////        } else if (dt instanceof ArrayType) {
////            return Arrays.toString((Object []) variant.getValue());
//        } else {
//            byte[] data = Bindings.getSerializerUnchecked(variant.getBinding()).serialize(variant.getValue());
//            m.reset();
//            m.update(data, 0, data.length);
//            return "\"" + new BigInteger(1, m.digest()).toString(16) + "\"";
//        }

    }

	//	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 = TransferableGraphUtils.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 = TransferableGraphUtils.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) {
			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(TransferableGraph1 graph, 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(graph, 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(TransferableGraph1 graph, 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(graph, 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(TransferableGraph1 graph, 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 = TransferableGraphUtils.findExternal(graph, "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, Integer> predicateURIs = new TreeMap<>();
		
		TIntArrayList rawStatements = TransferableGraphUtils.getStatements(graph, 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(graph, predicate);
			predicateURIs.put(predicateURI, object);
		}
		for (Entry<String, Integer> 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);
                }
			    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, Integer> 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));
		}
		
		if (DEBUG)
		    System.out.println(info.name + " : " + ownedOrdered.keySet());
		
		
		for (Entry<String, Integer> 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);
			}
		}		
		
		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<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(TransferableGraph1 graph) throws Exception {
	    log("Starting prettyPrint for TransferableGraph with " + graph.resourceCount + " resources, " + graph.identities + " identities, " + graph.statements.length + " statements and " + graph.values.length + " values");
	    
		for(Identity id : graph.identities) {
			if(id.definition instanceof Internal) {
				Internal internal = (Internal)id.definition;
				Identity parent = TransferableGraphUtils.getIdentity(graph, internal.parent);
				if(parent.definition instanceof External) {
				    log("Resolving internal identity " + id);
					String name = "BASE";
					ResourceInfo info = new ResourceInfo(true, name, id.resource, -1);
					info.aliasURI = TransferableGraphUtils.getURI(graph, id.resource);
					info.newResource = true;
					orderedInfos.put(name, info);
//					infos.put(id.resource, info);
					log("    which parent is external " + parent + " and has an aliasURI " + info.aliasURI);
					for(Identity child : TransferableGraphUtils.getChildren(graph, id)) {
						recurseURI(graph, child, name, info.resource);
					}
					log("    and has " + (infos.size() - 1) + " children");
				}
			} 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 = TransferableGraphUtils.getURI(graph, id.resource);
					
					log("    which was resolved as URI=" + uri + " and prefix " + prefix);
					
					ontologies.put(uri, prefix);
					
				} else if (ext.name.contains("-")) {
				    log("Resolving possible ontology " + ext);
					String uri = TransferableGraphUtils.getURI(graph, id.resource);
			        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=" + uri + " and prefix " + prefix);
                            ontologies.put(uri, prefix);
			        	}
			        }
				}
			}
		}
		
		// 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(graph, resource, todo);
		}
		for(ResourceInfo info : infos.valueCollection())
			discoverOwners(graph, 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;
                    }
                });
            }
        }

        // 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 = 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");
        
        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);
                if (elemToComponent != TransferableGraphUtils.NOT_FOUND) {
                    
                    Identity component = TransferableGraphUtils.getIdentity(graph, elemToComponent);
                    Identity internal = TransferableGraphUtils.getIdentity(graph, 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 = TransferableGraphUtils.getPossibleObject2(graph, 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, diagramConnetionToConnection);
                        if (connection != TransferableGraphUtils.NOT_FOUND) {
                            // Gather all inverse statements to construct unique name
                            List<String> nameParts = new ArrayList<>();
                            TIntArrayList statements = TransferableGraphUtils.getStatements(graph, connection);
                            for (int i = 0; i < statements.size(); i+=2) {
                                int predicate = statements.get(i);
                                Identity possibleInverse = TransferableGraphUtils.getIdentity(graph, 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, connection, possibleInverse);
                                            parentId = iPossibleInverse.parent;
                                        } else {
                                            LOGGER.error("THIS UNSUPPORTED for " + infoo + " " + iPossibleInverse);
                                        }
                                    } else if (possibleInverse.definition instanceof External) {
                                        External ePossibleInverse = (External) possibleInverse.definition;
                                        if (ePossibleInverse.name.equals("Inverse")) {
                                            inverseRelation = TransferableGraphUtils.getPossibleObject2(graph, connection, possibleInverse);
                                            parentId = ePossibleInverse.parent;
                                        } else {
                                            // This is not an inverse
//                                            LOGGER.error("THIS UNSUPPORTED TOO");
                                        }
                                    } else {
                                        LOGGER.error("UNSUPPORTED for " + infoo + " " );
                                    }
                                    if (inverseRelation != TransferableGraphUtils.NOT_FOUND) {
                                        // Ok found something
                                        Identity object = TransferableGraphUtils.getIdentity(graph, inverseRelation);
                                        Identity parent = TransferableGraphUtils.getIdentity(graph, 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 {
                                            LOGGER.error("UNSUPPORTED " + 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 {
                                            LOGGER.error("UNSUPPORTED " + infoo);
                                            throw new Error("UNSUPPORTED " + infoo);
                                        }
                                        String fullName = parentName + "_" + objectName;
                                        nameParts.add(fullName);
                                    } else {
                                        LOGGER.error("THIS IS ALSO UNSupported");
                                    }
                                } else {
                                    LOGGER.error("HERE");
                                }
                            }
                            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(Arrays.toString(graph.statements));
                            LOGGER.error("Subject -> Predicate : " + infoo.resource + " -> " + diagramConnetionToConnection.resource);
                        }
                    }
                }
            }
        }
        for (ResourceInfo info : infos.valueCollection()) {
            if (info.name.startsWith("blank")) {
                info.name = "blank" + findHash(graph, 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(graph, 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(graph, 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(graph, 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(TransferableGraph1 graph, 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(graph, 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(TransferableGraph1 graph, 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);
	            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(b, ignoreIdentifiers).prettyPrint(tg);
		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>]");
		} 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]));
		}
	}

    private static void log(String string) {
        if (LOGGER.isDebugEnabled() && DEBUG)
            LOGGER.debug(string);
    }

}