Fix for #191

docs/usage/queries.md

@@ -38,7 +38,7 @@ The queries can be provided in different formats:
 
 - one file with:
   - one query per line
-  - multi-line queries, separated by a separator line
+  - multi-line queries, separated by a separator
 - a folder with query files; one query per file
 
 The format is configured using the `format` parameter.
@@ -56,9 +56,9 @@ queries:
 
 ### Multi Line Queries
 
-The queries are stored in one file. Each query can span multiple lines and queries are separated by a separator line.
+The queries are stored in one file. Each query can span multiple lines and queries are separated by a separator.
 
-Let's look at an example, where the separator line is "###" (this is the default)
+Let's look at an example, where the separator is "###" (this is the default)
 
 ```
 QUERY  1 {
@@ -78,8 +78,8 @@ queries:
   format: "separator"
 ```
 
-However, you can also set the separator line in the configuration.
-For example if the separator is an empty line, the file can look like this:
+However, you can also set the separator in the configuration.
+For example, if you want to separate queries with empty lines, the queries-file can look like this:
 
 ```
 QUERY  1 {
@@ -91,7 +91,7 @@ still Query2
 }
 ```
 
-The configuration for this format is:
+For this configuration the given separator string can be empty:
 
 ```yaml
 queries:

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.IndexedQueryReader;
 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 IndexedQueryReader iqr;
 
     public FileLineQuerySource(String path) {
         super(path);
-        this.queryFile = new File(this.path);
+
         try {
-            this.size = FileUtils.countLines(this.queryFile);
+            iqr = IndexedQueryReader.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 iqr.size();
     }
 
     @Override
     public String getQuery(int index) throws IOException {
-        return FileUtils.readLineAt(index, this.queryFile);
+        return iqr.readQuery(index);
     }
 
     @Override
     public List<String> getAllQueries() throws IOException {
-        return Files.readAllLines(this.queryFile.toPath());
+        return iqr.readQueries();
     }
 }

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

@@ -1,23 +1,16 @@
 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.IndexedQueryReader;
 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
- * (multiline) queries that are separated by a separator line.
+ * (multiline) queries that are separated by a separator.
  *
  * @author frensing
  */
@@ -26,84 +19,53 @@ 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 IndexedQueryReader iqr;
 
+    /**
+     * This constructor indexes the queries inside the given file. It assumes, that the queries inside the file are
+     * separated with the default separator ('###').
+     *
+     * @param path path to the queries-file
+     */
     public FileSeparatorQuerySource(String path) {
         this(path, DEFAULT_SEPARATOR);
     }
 
+    /**
+     * This constructor indexes the queries inside the given file. Queries inside the file should be separated with the
+     * given separator string. If the separator string parameter is blank, it assumes that the queries inside the file
+     * are separated by blank lines.
+     *
+     * @param path path to the queries-file
+     * @param separator string with which the queries inside the file are separated
+     */
     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()) {
+                iqr = IndexedQueryReader.makeWithEmptyLines(path);
+            }
+            else {
+                iqr = IndexedQueryReader.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 iqr.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 iqr.readQuery(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 iqr.readQueries();
     }
-
 }

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.Arrays;
@@ -56,14 +54,7 @@ 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