add CsvReaderSettings

Preparation to add more complex CSV parsing rules.

pdb-api/src/main/java/org/lucares/pdb/api/UniqueStringIntegerPairs.java

@@ -119,6 +119,7 @@ public class UniqueStringIntegerPairs {
                 String line;
                 while ((line = reader.readLine()) != null) {
 
+                    // TODO use more efficient code to read the CSV -> improves startup time
                     final String[] tokens = line.split(Pattern.quote(SEPARATOR));
 
                     if (tokens.length == 2) {

pdb-ui/src/main/java/org/lucares/pdbui/CsvReaderSettings.java

@@ -0,0 +1,23 @@
+package org.lucares.pdbui;
+
+import org.lucares.utils.Preconditions;
+
+public class CsvReaderSettings {
+    private final byte separator;
+
+    public CsvReaderSettings(final byte separator) {
+        this.separator = separator;
+    }
+
+    public CsvReaderSettings(final char separator) {
+        Preconditions.checkTrue(separator == (byte) separator,
+                "Only separators that fulfill separator == (byte)separator are supported. "
+                        + "This restriction is because the parsing algorithm skips the overhead of "
+                        + "translating bytes to characters.");
+        this.separator = (byte) separator;
+    }
+
+    public byte getSeparator() {
+        return separator;
+    }
+}

pdb-ui/src/main/java/org/lucares/pdbui/CsvToEntryTransformer.java

@@ -17,14 +17,21 @@ class CsvToEntryTransformer {
      * Column header names starting with "-" will be ignored.
      */
     static final String COLUM_IGNORE_PREFIX = "-";
-    private static final int IGNORE_COLUMN = 0;
+    static final int IGNORE_COLUMN = 0;
+    private final ArrayBlockingQueue<Entries> queue;
+    private final CsvReaderSettings settings;
 
-    void readCSV(final InputStream in, final ArrayBlockingQueue<Entries> queue)
+    public CsvToEntryTransformer(final ArrayBlockingQueue<Entries> queue, final CsvReaderSettings settings) {
-            throws IOException, InterruptedException {
+        this.queue = queue;
+        this.settings = settings;
+    }
+
+    void readCSV(final InputStream in) throws IOException, InterruptedException {
         final int chunksize = 1000;
         Entries entries = new Entries(chunksize);
 
         final byte newline = '\n';
+        final byte separator = settings.getSeparator();
         final byte[] line = new byte[64 * 1024]; // max line length
         int offsetInLine = 0;
         int offsetInBuffer = 0;
@@ -68,7 +75,7 @@ class CsvToEntryTransformer {
                     offsetInLine = 0;
                     bytesInLine = 0;
                     separatorPositions.clear();
-                } else if (buffer[i] == ',') {
+                } else if (buffer[i] == separator) {
                     separatorPositions.add(offsetInLine + i - offsetInBuffer);
                 }
             }

pdb-ui/src/main/java/org/lucares/pdbui/IngestionHandler.java

@@ -65,8 +65,8 @@ public final class IngestionHandler implements Callable<Void> {
             handleInputStream(gzip);
         } else {
             in.reset();
-            final CsvToEntryTransformer csvTransformer = new CsvToEntryTransformer();
+            final CsvToEntryTransformer csvTransformer = new CsvToEntryTransformer(queue, new CsvReaderSettings(','));
-            csvTransformer.readCSV(in, queue);
+            csvTransformer.readCSV(in);
         }
     }