code: package it.unibz.inf.ontop.protege.query;
  
  /*
   * #%L
   * ontop-obdalib-core
   * %%
   * Copyright (C) 2009 - 2014 Free University of Bozen-Bolzano
   * %%
   * Licensed under the Apache License, Version 2.0 (the "License");
   * you may not use this file except in compliance with the License.
   * You may obtain a copy of the License at
   * 
   *      http://www.apache.org/licenses/LICENSE-2.0
   * 
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   * #L%
   */
  
  import it.unibz.inf.ontop.protege.utils.DialogUtils;
  import it.unibz.inf.ontop.protege.utils.EventListenerList;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import javax.annotation.Nonnull;
  import javax.annotation.Nullable;
  import java.io.*;
  import java.util.*;
  import java.util.stream.Collectors;
  import java.util.stream.Stream;
  
  public class QueryManager {
  
  	private static final Logger LOGGER = LoggerFactory.getLogger(QueryManager.class);
  
  	private final Item root = new Item(null, "Queries", null);
  
  	public Item getRoot() {
  		return root;
  	}
  
  	public class Item {
  		@Nullable
  		private final Item parent;
  		private final List<Item> children = new ArrayList<>();
  		@Nonnull
  		private String id;
  		@Nullable
  		private String queryString;
  
  		private Item(@Nullable Item parent, @Nonnull String id, @Nullable  String queryString) {
  			this.parent = parent;
  			this.id = id;
  			this.queryString = queryString == null ? null : queryString.trim();
  		}
  
  		@Override
  		public boolean equals(Object obj) {
  			if (obj instanceof Item) {
  				Item other = (Item)obj;
  				return this.parent == other.parent && this.id.equals(other.id);
  			}
  			return false;
  		}
  
  		@Override
  		public String toString() {
  			return "QueryManager.Item " + id + " > " + children;
  		}
  
  		public Item addGroupChild(String id) {
  			return addChild(id, null);
  		}
  
  		public Item addQueryChild(String id, String queryString) {
  			if (queryString == null)
  				throw new IllegalArgumentException("Query string cannot be null in a query.");
  
  			return addChild(id, queryString);
  		}
  
  		private Item addChild(String id, @Nullable String queryString) {
  			if (id == null || id.isEmpty())
  				throw new IllegalArgumentException("The query ID cannot be null or blank.");
  
  			if (isQuery())
  				throw new IllegalArgumentException("Cannot add entities to a query.");
  
  			Item item = new Item(this, id, queryString);
  
  			if (children.contains(item))
  				throw new IllegalArgumentException("The parent group already contains this group / query.");
  
  			children.add(item);
  			listeners.fire(l -> l.inserted(item, children.size() - 1));
  			return item;
  		}
  
  		public void removeChild(Item item) {
  			int indexInParent = children.indexOf(item);
  			if (indexInParent == -1)
  				throw new IllegalArgumentException("Cannot find the child");
  
  			children.remove(item);
  			listeners.fire(l -> l.removed(item, indexInParent));
  		}
  
  		public String getID() { return id; }
  
  		public void setID(String newId) {
  			if (parent == null)
  				throw new IllegalArgumentException("Cannot change the ID of the root");
  
  			if (parent.getChild(newId).isPresent())
  				throw new IllegalArgumentException("The parent group already contains this group / query.");
  
  			this.id = newId;
  			listeners.fire(l -> l.renamed(this, parent.children.indexOf(this)));
  		}
  
  		public Item getParent() { return parent; }
  
  		public boolean isQuery() { return queryString != null; }
  
  		public String getQueryString() { return queryString; }
  
  		public void setQueryString(String queryString) {
  			if (queryString == null)
  				throw new IllegalArgumentException("The query string cannot be null in a query.");
  
  			if (!children.isEmpty() || parent == null)
  				throw new IllegalArgumentException("Cannot set a query string for a group / root.");
  
  			this.queryString = queryString.trim();
  			listeners.fire(l -> l.changed(this, parent.children.indexOf(this)));
  		}
  
  		public Optional<Item> getChild(String id) {
  			for (Item child : children)
  				if (child.getID().equals(id))
  					return Optional.of(child);
  
  			return Optional.empty();
  		}
  
  		public int getIndexOfChild(Item child) {
  			return children.indexOf(child);
  		}
  
  		public Item getChild(int index) {
  			return children.get(index);
  		}
  
  		public int getChildCount() { return children.size(); }
  
  		public List<Item> getChildren() { return Collections.unmodifiableList(children); }
  	}
  
  
  	private final EventListenerList<QueryManagerListener> listeners = new EventListenerList<>();
  
  	/**
  	 * No need to remove listeners - this is handled by OBDAModelManager
  	 * @param listener
  	 */
  	public void addListener(QueryManagerListener listener) {
  		listeners.add(listener);
  	}
  
  
  
  	private static final String QUERY_GROUP = "QueryGroup";
  	private static final String QUERY_ITEM = "QueryItem";
  
  	private static final String QUERY_GROUP_TAG = "[" + QUERY_GROUP + "=\"%s\"]";
  	private static final String QUERY_ITEM_TAG = "[" + QUERY_ITEM + "=\"%s\"]";
  
  	private static final String START_COLLECTION_SYMBOL = "@collection [[";
  	private static final String END_COLLECTION_SYMBOL = "]]";
  
  	private static final String COMMENT_SYMBOL = ";";
  
  
  	public void store(File queriesFile) throws IOException {
  		DialogUtils.saveFileOrDeleteEmpty(root.getChildCount() == 0, queriesFile, file -> {
  			try (FileWriter writer = new FileWriter(file)) {
  				writer.write(root.getChildren().stream()
  						.flatMap(QueryManager::renderItem)
  						.collect(Collectors.joining("\n")));
  			}
  			catch (IOException e) {
  				throw new IOException(String.format("Error while saving the SPARQL queries to the file located at %s.\n" +
  						"Make sure you have the write permission at the location specified.", file.getAbsolutePath()));
  			}
  		}, LOGGER);
  	}
  
  	private static Stream<String> renderItem(Item item) {
  		return item.isQuery()
  				? Stream.of(String.format(QUERY_ITEM_TAG, item.getID()), item.getQueryString())
  				: Stream.concat(Stream.concat(
  						Stream.of(String.format(QUERY_GROUP_TAG, item.getID()) + " " + START_COLLECTION_SYMBOL),
  						item.children.stream()
  							.flatMap(QueryManager::renderItem)),
  					Stream.of(END_COLLECTION_SYMBOL));
  	}
  
  	public void clear() {
  		root.children.clear();
  	}
  
  	/**
  	 * Should not be called twice in a row without clear() in between.
  	 */
  
  	public void load(File queriesFile) throws IOException {
  		if (queriesFile.exists()) {
  			try (FileReader reader = new FileReader(queriesFile)) {
  				LineNumberReader lineNumberReader = new LineNumberReader(reader);
  				try {
  					String lastLine = readGroup(lineNumberReader, root);
  					if (lastLine != null)
  						throw new IOException("Unexpected file contents");
  				}
  				catch (Exception e) {
  					throw new IOException(String.format("Invalid syntax at line: %s", lineNumberReader.getLineNumber()), e);
  				}
  			}
  			catch (IOException ex) {
  				throw new IOException("Exception occurred while loading query document: " + queriesFile + "\n\n" + ex.getMessage());
  			}
  		}
  	}
  
  	private String readGroup(LineNumberReader lineNumberReader, Item group) throws IOException {
  		String line;
  		while (!isEndOfGroup(line = lineNumberReader.readLine())) {
  			if (!isEmptyLineOrComment(line)) {
  				if (line.contains(QUERY_GROUP)) {
  					String groupId = extractItemId(line);
  					Item subGroup = group.addGroupChild(groupId);
  					String lastLine = readGroup(lineNumberReader, subGroup);
  					if (lastLine == null)
  						throw new IOException("Unexpected EOF");
  				}
  				else if (line.contains(QUERY_ITEM)) {
  					String queryId = extractItemId(line);
  					String queryString = readQueryString(lineNumberReader);
  					group.addQueryChild(queryId, queryString);
  				}
  				else
  					throw new IOException("Expected a group or a query tag");
  			}
  		}
  		return line;
  	}
  
  	private String readQueryString(LineNumberReader lineNumberReader) throws IOException {
  		StringBuilder buffer = new StringBuilder();
  		String line;
  		while (!isEndOfQuery(line = lineNumberReader.readLine())) {
  			lineNumberReader.mark(100000);
  			buffer.append(line).append("\n");
  		}
  		lineNumberReader.reset(); // rewind back to the start of the last line
  		return buffer.toString();
  	}
  
  	private static boolean isEndOfGroup(String line) {
  		return line == null || line.trim().startsWith(END_COLLECTION_SYMBOL);
  	}
  
  	private static boolean isEndOfQuery(String line) {
  		return isEndOfGroup(line) || line.contains(QUERY_ITEM) || line.contains(QUERY_GROUP);
  	}
  
  	private static boolean isEmptyLineOrComment(String line) {
  		return line.isEmpty()
  				// A comment line is always started by a semi-colon (after spaces)
  				|| (line.contains(COMMENT_SYMBOL) && line.trim().indexOf(COMMENT_SYMBOL) == 0);
  	}
  
  	private static String extractItemId(String line) {
  		// IDs are enclosed in double quotation marks
  		return line.substring(line.indexOf('\"') + 1, line.lastIndexOf('\"'));
  	}
  }
  