Skip to content

Commit b25bd7c

Browse files
ctruedenctrueden
authored
Merge pull request #340 from scijava/stream-locations
Add stream locations
2 parents 6c094f7 + 183c2e4 commit b25bd7c

10 files changed

+644
-19
lines changed

‎src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java

+105
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,105 @@
1+
/*
2+
* #%L
3+
* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
31+
32+
package org.scijava.io.handle;
33+
34+
import java.io.IOException;
35+
36+
import org.scijava.io.location.Location;
37+
38+
public abstract class AbstractSeekableStreamHandle<L extends Location> extends
39+
AbstractStreamHandle<L> implements SeekableStreamHandle<L>
40+
{
41+
42+
private long jumpCutoff = 10000;
43+
44+
@Override
45+
public void seek(final long pos) throws IOException {
46+
47+
// how much and which direction we have to jump
48+
final long delta = pos - offset();
49+
50+
if (delta == 0) {
51+
return;
52+
// nothing to do
53+
}
54+
else if (delta > 0) {
55+
// offset position is "downstream"
56+
57+
// try to reconnect instead of linearly reading large chunks
58+
if (recreatePossible() && delta > jumpCutoff) {
59+
recreateStreamFromPos(pos);
60+
}
61+
else {
62+
jump(delta);
63+
}
64+
65+
}
66+
else { // delta < 0
67+
// need to recreate the stream
68+
if (recreatePossible()) {
69+
recreateStreamFromPos(pos);
70+
}
71+
else {
72+
resetStream();
73+
jump(pos);
74+
}
75+
}
76+
setOffset(pos);
77+
}
78+
79+
/**
80+
* Recreates the internal input stream available through {@link #in()}, so
81+
* that it starts from the specified position.
82+
*
83+
* @param pos
84+
* @throws IOException
85+
*/
86+
protected abstract void recreateStreamFromPos(long pos) throws IOException;
87+
88+
/**
89+
* In some implementations of this class, the ability to recreate the stream
90+
* depends on external factors (e.g. server support). This influences a
91+
*
92+
* @return if recreate is actually possible.
93+
* @throws IOException
94+
*/
95+
protected abstract boolean recreatePossible() throws IOException;
96+
97+
/**
98+
* Sets the maximum of bytes which are read from the stream when seeking
99+
* forward. Any larger number will result in a call to
100+
* {@link #recreateStreamFromPos(long)}.
101+
*/
102+
protected void setJumpCutoff(long jumpCutoff) {
103+
this.jumpCutoff = jumpCutoff;
104+
}
105+
}

‎src/main/java/org/scijava/io/handle/AbstractStreamHandle.java

+65
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,65 @@
1+
/*
2+
* #%L
3+
* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
31+
32+
package org.scijava.io.handle;
33+
34+
import org.scijava.io.location.Location;
35+
36+
/**
37+
* Abstract base class for {@link StreamHandle} implementations.
38+
*
39+
* @author Curtis Rueden
40+
* @author Melissa Linkert
41+
*/
42+
public abstract class AbstractStreamHandle<L extends Location> extends
43+
AbstractDataHandle<L> implements StreamHandle<L>
44+
{
45+
46+
// -- Fields --
47+
48+
/** Current position within the stream(s). */
49+
private long offset;
50+
51+
// -- StreamHandle methods --
52+
53+
@Override
54+
public void setOffset(final long offset) {
55+
this.offset = offset;
56+
}
57+
58+
// -- DataHandle methods --
59+
60+
@Override
61+
public long offset() {
62+
return offset;
63+
}
64+
65+
}

‎src/main/java/org/scijava/io/handle/DataHandle.java

+10-12
Original file line numberDiff line numberDiff line change
@@ -350,10 +350,7 @@ default String findString(final boolean saveString, final int blockSize,
350350
final StringBuilder out = new StringBuilder();
351351
final long startPos = offset();
352352
long bytesDropped = 0;
353-
final long inputLen = length();
354-
long maxLen = inputLen - startPos;
355-
final boolean tooLong = saveString && maxLen > MAX_SEARCH_SIZE;
356-
if (tooLong) maxLen = MAX_SEARCH_SIZE;
353+
final long maxLen = saveString ? MAX_SEARCH_SIZE : Long.MAX_VALUE;
357354
boolean match = false;
358355
int maxTermLen = 0;
359356
for (final String term : terminators) {
@@ -366,7 +363,10 @@ default String findString(final boolean saveString, final int blockSize,
366363
new DataHandleInputStream<>(this), getEncoding());
367364
final char[] buf = new char[blockSize];
368365
long loc = 0;
369-
while (loc < maxLen && offset() < length() - 1) {
366+
int r = 0;
367+
368+
// NB: we need at least 2 bytes to read a char
369+
while (loc < maxLen && ((r = in.read(buf, 0, blockSize)) > 1)) {
370370
// if we're not saving the string, drop any old, unnecessary output
371371
if (!saveString) {
372372
final int outLen = out.length();
@@ -378,16 +378,12 @@ default String findString(final boolean saveString, final int blockSize,
378378
bytesDropped += dropIndex;
379379
}
380380
}
381-
382-
// read block from stream
383-
final int r = in.read(buf, 0, blockSize);
384-
if (r <= 0) throw new IOException("Cannot read from stream: " + r);
385-
386381
// append block to output
387382
out.append(buf, 0, r);
388383

389384
// check output, returning smallest possible string
390-
int min = Integer.MAX_VALUE, tagLen = 0;
385+
int min = Integer.MAX_VALUE;
386+
int tagLen = 0;
391387
for (final String t : terminators) {
392388
final int len = t.length();
393389
final int start = (int) (loc - bytesDropped - len);
@@ -415,7 +411,9 @@ default String findString(final boolean saveString, final int blockSize,
415411
}
416412

417413
// no match
418-
if (tooLong) throw new IOException("Maximum search length reached.");
414+
if (loc > MAX_SEARCH_SIZE) {
415+
throw new IOException("Maximum search length reached.");
416+
}
419417
return saveString ? out.toString() : null;
420418
}
421419

‎src/main/java/org/scijava/io/handle/ResettableStreamHandle.java

+72
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,72 @@
1+
/*
2+
* #%L
3+
* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
31+
32+
package org.scijava.io.handle;
33+
34+
import java.io.IOException;
35+
import java.io.InputStream;
36+
import java.io.OutputStream;
37+
38+
import org.scijava.io.location.Location;
39+
40+
/**
41+
* A {@link DataHandle} backed by an {@link InputStream} and/or
42+
* {@link OutputStream}. Supports resetting the handle to the start of the
43+
* internal stream(s).
44+
*/
45+
public interface ResettableStreamHandle<L extends Location> extends
46+
StreamHandle<L>
47+
{
48+
49+
@Override
50+
default void seek(final long pos) throws IOException {
51+
final long off = offset();
52+
if (pos == off) return; // nothing to do
53+
if (pos > off) {
54+
// jump from the current offset
55+
jump(pos - off);
56+
}
57+
else {
58+
// jump from the beginning of the stream
59+
resetStream();
60+
jump(pos);
61+
}
62+
setOffset(pos);
63+
}
64+
65+
/**
66+
* Resets the stream to its start.
67+
*
68+
* @throws IOException If something goes wrong with the reset
69+
*/
70+
@Override
71+
void resetStream() throws IOException;
72+
}

‎src/main/java/org/scijava/io/handle/SeekableStreamHandle.java

+53
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,53 @@
1+
/*
2+
* #%L
3+
* SciJava Common shared library for SciJava software.
4+
* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
31+
32+
package org.scijava.io.handle;
33+
34+
import java.io.IOException;
35+
import java.io.InputStream;
36+
import java.io.OutputStream;
37+
38+
import org.scijava.io.location.Location;
39+
40+
/**
41+
* A {@link DataHandle} backed by an {@link InputStream} and/or
42+
* {@link OutputStream}. Supports seeking to an arbitrary position within the
43+
* stream.
44+
*
45+
* @author Gabriel Einsdorf
46+
*/
47+
public interface SeekableStreamHandle<L extends Location> extends
48+
ResettableStreamHandle<L>
49+
{
50+
51+
@Override
52+
void seek(long pos) throws IOException;
53+
}

0 commit comments

Comments
 (0)