Merge pull request #166 from scijava/robust-io

A robust general framework for I/O

Author: ctrueden

src/main/java/org/scijava/Typed.java

@@ -42,9 +42,8 @@ public interface Typed<T> {
 	/**
 	 * Gets whether this object is compatible with the given data object.
 	 * <p>
-	 * Typically, this will be the case when {@code data.getClass()} is assignable
-	 * to the type associated with the object (i.e., the one returned by
-	 * {@link #getType()}). But individual implementations may have other
+	 * By default, this method will return {@code true} always, since the type is
+	 * known to be compatible. But individual implementations may have other
 	 * requirements beyond class assignability.
 	 * </p>
 	 */

src/main/java/org/scijava/io/AbstractDataHandle.java

@@ -0,0 +1,275 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2015 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+
+import org.scijava.plugin.AbstractWrapperPlugin;
+
+/**
+ * Abstract base class for {@link DataHandle} plugins.
+ *
+ * @author Curtis Rueden
+ */
+public abstract class AbstractDataHandle<L extends Location> extends
+	AbstractWrapperPlugin<L> implements DataHandle<L>
+{
+
+	// -- Constants --
+
+	/** Block size to use when searching through the stream. */
+	private static final int DEFAULT_BLOCK_SIZE = 256 * 1024; // 256 KB
+
+	/** Maximum number of bytes to search when searching through the stream. */
+	private static final int MAX_SEARCH_SIZE = 512 * 1024 * 1024; // 512 MB
+
+	// -- Fields --
+
+	private ByteOrder order = ByteOrder.BIG_ENDIAN;
+	private String encoding = "UTF-8";
+
+	// -- DataHandle methods --
+
+	@Override
+	public ByteOrder getOrder() {
+		return order;
+	}
+
+	@Override
+	public boolean isLittleEndian() {
+		return getOrder() == ByteOrder.LITTLE_ENDIAN;
+	}
+
+	@Override
+	public void setOrder(final ByteOrder order) {
+		this.order = order;
+	}
+
+	@Override
+	public void setOrder(final boolean little) {
+		setOrder(little ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN);
+	}
+
+	@Override
+	public String getEncoding() {
+		return encoding;
+	}
+
+	@Override
+	public void setEncoding(final String encoding) {
+		this.encoding = encoding;
+	}
+
+	@Override
+	public int read(final ByteBuffer buf) throws IOException {
+		return read(buf, buf.remaining());
+	}
+
+	@Override
+	public int read(final ByteBuffer buf, final int len)
+		throws IOException
+	{
+		final int n;
+		if (buf.hasArray()) {
+			// read directly into the array
+			n = read(buf.array(), buf.arrayOffset(), len);
+		}
+		else {
+			// read into a temporary array, then copy
+			final byte[] b = new byte[len];
+			n = read(b);
+			buf.put(b, 0, n);
+		}
+		return n;
+	}
+
+	@Override
+	public void write(final ByteBuffer buf) throws IOException {
+		write(buf, buf.remaining());
+	}
+
+	@Override
+	public void write(final ByteBuffer buf, final int len)
+		throws IOException
+	{
+		if (buf.hasArray()) {
+			// write directly from the buffer's array
+			write(buf.array(), buf.arrayOffset(), len);
+		}
+		else {
+			// copy into a temporary array, then write
+			final byte[] b = new byte[len];
+			buf.get(b);
+			write(b);
+		}
+	}
+
+	@Override
+	public String readCString() throws IOException {
+		final String line = findString("\0");
+		return line.length() == 0 ? null : line;
+	}
+
+	@Override
+	public String readString(int n) throws IOException {
+		final long avail = length() - offset();
+		if (n > avail) n = (int) avail;
+		final byte[] b = new byte[n];
+		readFully(b);
+		return new String(b, encoding);
+	}
+
+	@Override
+	public String readString(final String lastChars) throws IOException {
+		if (lastChars.length() == 1) return findString(lastChars);
+		final String[] terminators = new String[lastChars.length()];
+		for (int i = 0; i < terminators.length; i++) {
+			terminators[i] = lastChars.substring(i, i + 1);
+		}
+		return findString(terminators);
+	}
+
+	@Override
+	public String findString(final String... terminators) throws IOException {
+		return findString(true, DEFAULT_BLOCK_SIZE, terminators);
+	}
+
+	@Override
+	public String findString(final boolean saveString,
+		final String... terminators) throws IOException
+	{
+		return findString(saveString, DEFAULT_BLOCK_SIZE, terminators);
+	}
+
+	@Override
+	public String findString(final int blockSize, final String... terminators)
+		throws IOException
+	{
+		return findString(true, blockSize, terminators);
+	}
+
+	@Override
+	public String findString(final boolean saveString, final int blockSize,
+		final String... terminators) throws IOException
+	{
+		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;
+		boolean match = false;
+		int maxTermLen = 0;
+		for (final String term : terminators) {
+			final int len = term.length();
+			if (len > maxTermLen) maxTermLen = len;
+		}
+
+		@SuppressWarnings("resource")
+		final InputStreamReader in =
+			new InputStreamReader(new DataHandleInputStream<L>(this), getEncoding());
+		final char[] buf = new char[blockSize];
+		long loc = 0;
+		while (loc < maxLen && offset() < length() - 1) {
+			// if we're not saving the string, drop any old, unnecessary output
+			if (!saveString) {
+				final int outLen = out.length();
+				if (outLen >= maxTermLen) {
+					final int dropIndex = outLen - maxTermLen + 1;
+					final String last = out.substring(dropIndex, outLen);
+					out.setLength(0);
+					out.append(last);
+					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;
+			for (final String t : terminators) {
+				final int len = t.length();
+				final int start = (int) (loc - bytesDropped - len);
+				final int value = out.indexOf(t, start < 0 ? 0 : start);
+				if (value >= 0 && value < min) {
+					match = true;
+					min = value;
+					tagLen = len;
+				}
+			}
+
+			if (match) {
+				// reset stream to proper location
+				seek(startPos + bytesDropped + min + tagLen);
+
+				// trim output string
+				if (saveString) {
+					out.setLength(min + tagLen);
+					return out.toString();
+				}
+				return null;
+			}
+
+			loc += r;
+		}
+
+		// no match
+		if (tooLong) throw new IOException("Maximum search length reached.");
+		return saveString ? out.toString() : null;
+	}
+
+	// -- InputStream look-alikes --
+
+	@Override
+	public int read(byte[] b) throws IOException {
+		return read(b, 0, b.length);
+	}
+
+	@Override
+	public long skip(final long n) throws IOException {
+		if (n < 0) return 0;
+		final long remain = length() - offset();
+		final long num = n < remain ? n : remain;
+		seek(offset() + num);
+		return num;
+	}
+
+}

src/main/java/org/scijava/io/AbstractLocation.java

@@ -0,0 +1,50 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2015 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import java.net.URI;
+
+/**
+ * Abstract base class for {@link Location} implementations.
+ * 
+ * @author Curtis Rueden
+ */
+public abstract class AbstractLocation implements Location {
+
+	// -- Location methods --
+
+	@Override
+	public URI getURI() {
+		return null;
+	}
+
+}