Fix for #191

iguana.corecontroller/src/main/java/org/aksw/iguana/cc/query/source/impl/FileLineQuerySource.java

@@ -1,13 +1,11 @@
 package org.aksw.iguana.cc.query.source.impl;
 
 import org.aksw.iguana.cc.query.source.QuerySource;
-import org.aksw.iguana.cc.utils.FileUtils;
+import org.aksw.iguana.cc.utils.IndexedLineReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.util.List;
 
 /**
@@ -18,32 +16,30 @@
 public class FileLineQuerySource extends QuerySource {
     private static final Logger LOGGER = LoggerFactory.getLogger(FileLineQuerySource.class);
 
-    protected File queryFile;
-
-    protected int size;
+    private IndexedLineReader ilr;
 
     public FileLineQuerySource(String path) {
         super(path);
-        this.queryFile = new File(this.path);
+
         try {
-            this.size = FileUtils.countLines(this.queryFile);
+            ilr = IndexedLineReader.make(path);
         } catch (IOException e) {
-            LOGGER.error("Could not read queries");
+            LOGGER.error("Failed to read this file for the queries: " + path + "\n" + e);
         }
     }
 
     @Override
     public int size() {
-        return this.size;
+        return ilr.size();
     }
 
     @Override
     public String getQuery(int index) throws IOException {
-        return FileUtils.readLineAt(index, this.queryFile);
+        return ilr.readLine(index);
     }
 
     @Override
     public List<String> getAllQueries() throws IOException {
-        return Files.readAllLines(this.queryFile.toPath());
+        return ilr.readLines();
     }
 }

iguana.corecontroller/src/main/java/org/aksw/iguana/cc/query/source/impl/FileSeparatorQuerySource.java

@@ -1,19 +1,12 @@
 package org.aksw.iguana.cc.query.source.impl;
 
 import org.aksw.iguana.cc.query.source.QuerySource;
-import org.aksw.iguana.cc.utils.FileUtils;
+import org.aksw.iguana.cc.utils.IndexedLineReader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.nio.file.Files;
-import java.util.ArrayList;
-import java.util.LinkedList;
 import java.util.List;
-import java.util.stream.Stream;
 
 /**
  * The FileSeparatorQuerySource reads queries from a file with
@@ -26,84 +19,39 @@ public class FileSeparatorQuerySource extends QuerySource {
 
     private static final String DEFAULT_SEPARATOR = "###";
 
-    protected File queryFile;
-    protected String separator;
-    protected int size;
-
-    private List<Integer> separatorPositions;
+    private IndexedLineReader ilr;
 
     public FileSeparatorQuerySource(String path) {
         this(path, DEFAULT_SEPARATOR);
     }
 
     public FileSeparatorQuerySource(String path, String separator) {
         super(path);
-        this.queryFile = new File(this.path);
-        this.separator = separator;
-
-        indexFile();
-    }
 
-    private void indexFile() {
-        this.separatorPositions = new LinkedList<>();
-        int separatorCount = 0;
-        try (BufferedReader reader = FileUtils.getBufferedReader(this.queryFile)) {
-            int index = 0;
-            String line;
-            this.separatorPositions.add(-1);
-            while ((line = reader.readLine()) != null) {
-                if (line.equals(this.separator)) {
-                    separatorCount++;
-                    this.separatorPositions.add(index);
-                }
-                index++;
+        try {
+            if(separator.isBlank()) {
+                ilr = IndexedLineReader.makeWithBlankLines(path);
+            }
+            else {
+                ilr = IndexedLineReader.makeWithStringSeparator(path, separator);
             }
-            this.separatorPositions.add(index);
         } catch (IOException e) {
-            LOGGER.error("Could not read queries");
+            LOGGER.error("Failed to read this file for the queries: " + path + "\n" + e);
         }
-
-        this.size = separatorCount + 1;
     }
 
     @Override
     public int size() {
-        return this.size;
+        return ilr.size();
     }
 
     @Override
     public String getQuery(int index) throws IOException {
-        int start = this.separatorPositions.get(index) + 1;
-        int end = this.separatorPositions.get(index + 1);
-
-        try (Stream<String> lines = Files.lines(this.queryFile.toPath())) {
-            return lines.skip(start)
-                    .limit(end - start)
-                    .reduce((a, b) -> a + b)
-                    .get();
-        } catch (FileNotFoundException e) {
-            LOGGER.error("Could not read queries");
-        }
-        return null;
+        return ilr.readLine(index);
     }
 
     @Override
     public List<String> getAllQueries() throws IOException {
-        try (BufferedReader reader = FileUtils.getBufferedReader(this.queryFile)) {
-            List<String> queries = new ArrayList<>(this.size);
-            String line;
-            StringBuilder query = new StringBuilder();
-            while ((line = reader.readLine()) != null) {
-                if (line.equals(this.separator)) {
-                    queries.add(query.toString());
-                    query = new StringBuilder();
-                } else {
-                    query.append(line);
-                }
-            }
-            queries.add(query.toString());
-            return queries;
-        }
+        return ilr.readLines();
     }
-
 }

iguana.corecontroller/src/main/java/org/aksw/iguana/cc/query/source/impl/FolderQuerySource.java

@@ -5,9 +5,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -52,14 +50,7 @@ public int size() {
 
     @Override
     public String getQuery(int index) throws IOException {
-        try (BufferedReader reader = new BufferedReader(new FileReader(this.files[index]))) {
-            StringBuilder query = new StringBuilder();
-            String line;
-            while ((line = reader.readLine()) != null) {
-                query.append(line);
-            }
-            return query.toString();
-        }
+        return FileUtils.readFile(files[index].getAbsolutePath());
     }
 
     @Override

iguana.corecontroller/src/main/java/org/aksw/iguana/cc/utils/FileUtils.java

@@ -14,74 +14,81 @@
 public class FileUtils {
 
 	/**
-	 * Counts the lines in a file efficiently. Props goes to:
-	 * <a href="http://stackoverflow.com/a/453067/2917596">http://stackoverflow.com/a/453067/2917596</a>
+	 * Counts the lines in a file efficiently. (only if the line ending is "\n") <br/>
+	 * Source: <a href="http://stackoverflow.com/a/453067/2917596">http://stackoverflow.com/a/453067/2917596</a>
 	 *
-	 * @param filename File to count lines of
-	 * @return No. of lines in File
+	 * @param filename file to count lines of
+	 * @return number of lines in the given file
 	 * @throws IOException
 	 */
 	public static int countLines(File filename) throws IOException {
-		try (InputStream is = new BufferedInputStream(new FileInputStream(filename))) {
-
-			byte[] c = new byte[1024];
-			int count = 0;
-			int readChars;
-			boolean empty = true;
-			byte lastChar = '\n';
-			while ((readChars = is.read(c)) != -1) {
-				for (int i = 0; i < readChars; ++i) {
-					if (c[i] == '\n') {
-						// Check if line was empty
-						if (lastChar != '\n') {
-							++count;
+		if(getLineEnding((filename.getAbsolutePath())).equals("\n")) {
+			final int BUFFER_SIZE = 8192;
+			try (FileInputStream fis = new FileInputStream(filename)) {
+				InputStream is = new BufferedInputStream(fis, BUFFER_SIZE);
+				byte[] c = new byte[BUFFER_SIZE];
+				int count = 0;
+				int readChars = 0;
+				boolean empty = true;
+				byte lastChar = '\n';
+				while ((readChars = is.read(c)) != -1) {
+					for (int i = 0; i < readChars; ++i) {
+						if (c[i] == '\n') {
+							// Check if line was empty
+							if (lastChar != '\n') {
+								++count;
+							}
+						} else {
+							empty = false;
 						}
-					} else {
-						empty = false;
+						lastChar = c[i];
 					}
-					lastChar = c[i];
 				}
+				if (lastChar != '\n') {
+					count++;
+				}
+				return (count == 0 && !empty) ? 1 : count;
 			}
-			if (lastChar != '\n') {
-				count++;
+		} else {
+			String line = "";
+			int count = 0;
+			try(FileReader fr = new FileReader(filename)) {
+				BufferedReader br = new BufferedReader(fr);
+				while ((line = br.readLine()) != null) {
+					if (!line.isEmpty()) {
+						count++;
+					}
+				}
 			}
-			return (count == 0 && !empty) ? 1 : count;
+			return count;
 		}
 	}
 
 	/**
-	 * Returns a line at a given position of a File
-	 * 
-	 * @param pos      line which should be returned
-	 * @param filename File in which the queries are stated
-	 * @return line at pos
+	 * Returns a line at a given position of a File. <br/>
+	 * This method ignores every empty line, therefore the parameter <code>pos</code> references the n-th non-empty line.
+	 *
+	 * @param index the position of a non-empty line which should be returned
+	 * @param file 	the file to read from
+	 * @return the line at the given position
 	 * @throws IOException
 	 */
-	public static String readLineAt(int pos, File filename) throws IOException {
-		try (InputStream is = new BufferedInputStream(new FileInputStream(filename))) {
-			StringBuilder line = new StringBuilder();
+	public static String readLineAt(int index, File file) throws IOException {
+		String line = "";
+		int count = 0;
 
-			byte[] c = new byte[1024];
-			int count = 0;
-			int readChars;
-			byte lastChar = '\n';
-			while ((readChars = is.read(c)) != -1) {
-				for (int i = 0; i < readChars; ++i) {
-					if (c[i] == '\n') {
-						// Check if line was empty
-						if (lastChar != '\n') {
-							++count;
-						}
-					} else if (count == pos) {
-						// Now the line
-						line.append((char) c[i]);
+		try(FileReader fr = new FileReader(file)) {
+			BufferedReader br = new BufferedReader(fr);
+			while ((line = br.readLine()) != null) {
+				if (!line.isBlank()) {
+					if (count == index) {
+						return line;
 					}
-					lastChar = c[i];
+					count++;
 				}
 			}
-
-			return line.toString();
-		} 
+		}
+		return "";
 	}
 
 	public static int getHashcodeFromFileContent(String filepath) {
@@ -100,6 +107,40 @@ public static String readFile(String path) throws IOException {
 		return new String(encoded, StandardCharsets.UTF_8);
 	}
 
+	/**
+	 * This method detects and returns the line-ending used in a file. <br/>
+	 * It reads the whole first line until it detects one of the following line-endings:
+	 * <ul>
+	 *     <li>\r\n - Windows</li>
+	 *     <li>\n - Linux</li>
+	 *     <li>\r - old macOS</li>
+	 * </ul>
+	 *
+	 * If the file doesn't contain a line ending, it defaults to <code>System.lineSeparator()</code>.
+	 *
+	 * @param filepath this string that contains the path of the file
+	 * @return the line ending used in the given file
+	 * @throws IOException
+	 */
+	public static String getLineEnding(String filepath) throws IOException {
+		try(FileReader fr = new FileReader(filepath)) {
+			BufferedReader br = new BufferedReader(fr);
+			char c;
+			while ((c = (char) br.read()) != (char) -1) {
+				if (c == '\n')
+					return "\n";
+				else if (c == '\r') {
+					if ((char) br.read() == '\n')
+						return "\r\n";
+					return "\r";
+				}
+			}
+		}
+
+		// fall back if there is no line end in the file
+		return System.lineSeparator();
+	}
+
 	public static BufferedReader getBufferedReader(File queryFile) throws FileNotFoundException {
 		return new BufferedReader(new FileReader(queryFile));
 	}