DataHandle: fix findString(..) and support handles with unknown length

The findString(..) method used to require the exact length of the
handle, this length can be unknown, e.g. for compressed handles.
This is	no longer the case.

Author: gab1one

Diff for: src/main/java/org/scijava/io/handle/DataHandle.java

@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -48,7 +48,7 @@
 /**
  * A <em>data handle</em> is a plugin which provides both streaming and random
  * access to bytes at a {@link Location} (e.g., files or arrays).
- * 
+ *
  * @author Curtis Rueden
  * @see DataHandleInputStream
  * @see DataHandleOutputStream
@@ -58,7 +58,7 @@ public interface DataHandle<L extends Location> extends WrapperPlugin<L>,
 {
 
 	public enum ByteOrder {
-		LITTLE_ENDIAN, BIG_ENDIAN
+			LITTLE_ENDIAN, BIG_ENDIAN
 	}
 
 	/** Default block size to use when searching through the stream. */
@@ -75,15 +75,15 @@ public enum ByteOrder {
 
 	/**
 	 * Tests whether this handle's location actually exists at the source.
-	 * 
+	 *
 	 * @return True if the location exists; false if not.
 	 * @throws IOException If something goes wrong with the existence check.
 	 */
 	boolean exists() throws IOException;
 
 	/**
 	 * Gets the last modified timestamp of the location.
-	 * 
+	 *
 	 * @return The last modified timestamp, or null if the handle does not support
 	 *         this feature or if the location does not exist.
 	 * @throws IOException If something goes wrong with the last modified check.
@@ -107,7 +107,7 @@ default Date lastModified() throws IOException {
 	 * the checksum is still the same, the contents are highly likely to be
 	 * unchanged.
 	 * </p>
-	 * 
+	 *
 	 * @return The checksum, or null if the handle does not support this feature.
 	 * @throws IOException If something goes wrong when accessing the checksum.
 	 */
@@ -126,22 +126,22 @@ default String checksum() throws IOException {
 
 	/**
 	 * Returns the length of the data in bytes.
-	 * 
+	 *
 	 * @return The length, or -1 if the length is unknown.
 	 */
 	long length() throws IOException;
 
 	/**
 	 * Sets the new length of the handle.
-	 * 
+	 *
 	 * @param length New length.
 	 * @throws IOException If there is an error changing the handle's length.
 	 */
 	void setLength(long length) throws IOException;
 
 	/**
-	 * Gets the number of bytes which can be read from, or written to, the
-	 * data handle, bounded by the specified number of bytes.
+	 * Gets the number of bytes which can be read from, or written to, the data
+	 * handle, bounded by the specified number of bytes.
 	 * <p>
 	 * In the case of reading, attempting to read the returned number of bytes is
 	 * guaranteed not to throw {@link EOFException}. However, be aware that the
@@ -161,8 +161,8 @@ default String checksum() throws IOException {
 	 * </p>
 	 *
 	 * @param count Desired number of bytes to read/write.
-	 * @return The actual number of bytes which could be read/written,
-	 *         which might be less than the requested value.
+	 * @return The actual number of bytes which could be read/written, which might
+	 *         be less than the requested value.
 	 * @throws IOException If something goes wrong with the check.
 	 */
 	default long available(final long count) throws IOException {
@@ -172,7 +172,7 @@ default long available(final long count) throws IOException {
 
 	/**
 	 * Ensures that the handle has sufficient bytes available to read.
-	 * 
+	 *
 	 * @param count Number of bytes to read.
 	 * @see #available(long)
 	 * @throws EOFException If there are insufficient bytes available.
@@ -187,7 +187,7 @@ default void ensureReadable(final long count) throws IOException {
 	/**
 	 * Ensures that the handle has the correct length to be written to, and
 	 * extends it as required.
-	 * 
+	 *
 	 * @param count Number of bytes to write.
 	 * @return {@code true} if the handle's length was sufficient, or
 	 *         {@code false} if the handle's length required an extension.
@@ -271,7 +271,7 @@ default String readString(final int n) throws IOException {
 
 	/**
 	 * Reads a string ending with one of the characters in the given string.
-	 * 
+	 *
 	 * @see #findString(String...)
 	 */
 	default String readString(final String lastChars) throws IOException {
@@ -285,7 +285,7 @@ default String readString(final String lastChars) throws IOException {
 
 	/**
 	 * Reads a string ending with one of the given terminating substrings.
-	 * 
+	 *
 	 * @param terminators The strings for which to search.
 	 * @return The string from the initial position through the end of the
 	 *         terminating sequence, or through the end of the stream if no
@@ -350,10 +350,7 @@ default String findString(final boolean saveString, final int blockSize,
 		final StringBuilder out = new StringBuilder();
 		final long startPos = offset();
 		long bytesDropped = 0;
-		final long inputLen = length();
-		long maxLen = inputLen - startPos;
-		final boolean tooLong = saveString && maxLen > MAX_SEARCH_SIZE;
-		if (tooLong) maxLen = MAX_SEARCH_SIZE;
+		final long maxLen = saveString ? MAX_SEARCH_SIZE : Long.MAX_VALUE;
 		boolean match = false;
 		int maxTermLen = 0;
 		for (final String term : terminators) {
@@ -366,7 +363,10 @@ default String findString(final boolean saveString, final int blockSize,
 			new DataHandleInputStream<>(this), getEncoding());
 		final char[] buf = new char[blockSize];
 		long loc = 0;
-		while (loc < maxLen && offset() < length() - 1) {
+		int r = 0;
+
+		// NB: we need at least 2 bytes to read a char
+		while (loc < maxLen && ((r = in.read(buf, 0, blockSize)) > 1)) {
 			// if we're not saving the string, drop any old, unnecessary output
 			if (!saveString) {
 				final int outLen = out.length();
@@ -378,16 +378,12 @@ default String findString(final boolean saveString, final int blockSize,
 					bytesDropped += dropIndex;
 				}
 			}
-
-			// read block from stream
-			final int r = in.read(buf, 0, blockSize);
-			if (r <= 0) throw new IOException("Cannot read from stream: " + r);
-
 			// append block to output
 			out.append(buf, 0, r);
 
 			// check output, returning smallest possible string
-			int min = Integer.MAX_VALUE, tagLen = 0;
+			int min = Integer.MAX_VALUE;
+			int tagLen = 0;
 			for (final String t : terminators) {
 				final int len = t.length();
 				final int start = (int) (loc - bytesDropped - len);
@@ -415,7 +411,9 @@ default String findString(final boolean saveString, final int blockSize,
 		}
 
 		// no match
-		if (tooLong) throw new IOException("Maximum search length reached.");
+		if (loc > MAX_SEARCH_SIZE) {
+			throw new IOException("Maximum search length reached.");
+		}
 		return saveString ? out.toString() : null;
 	}