Typekpb patch 1 (replacing samtools#725) (samtools#883)

* seek() checks for negative position argument value
* tests

src/main/java/htsjdk/samtools/seekablestream/ByteArraySeekableStream.java

@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2016 The Broad Institute
+ * Copyright (c) 2015 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -24,13 +24,11 @@
 
 package htsjdk.samtools.seekablestream;
 
-import htsjdk.samtools.seekablestream.SeekableStream;
-
 import java.io.IOException;
 
 /**
-* Created by vadim on 23/03/2015.
-*/
+ * Created by vadim on 23/03/2015.
+ */
 public class ByteArraySeekableStream extends SeekableStream {
     private byte[] bytes;
     private long position = 0;
@@ -51,21 +49,27 @@ public long position() throws IOException {
 
     @Override
     public void seek(long position) throws IOException {
-        this.position = position;
+        if (position < 0) {
+            throw new IllegalArgumentException("Cannot seek to a negative position, position=" + position + ".");
+        } else {
+            this.position = position;
+        }
     }
 
     @Override
     public int read() throws IOException {
-        if (position < bytes.length)
+        if (position < bytes.length) {
             return 0xFF & bytes[((int) position++)];
-        else return -1;
+        } else {
+            return -1;
+        }
     }
 
     @Override
     public int read(byte[] b, int off, int len) throws IOException {
         if (b == null) {
             throw new NullPointerException();
-        } else if (off < 0 || len < 0 || len > b.length - off) {
+        } else if (off < 0 || len < 0 || len + off > b.length) {
             throw new IndexOutOfBoundsException();
         }
         if (position >= bytes.length) {
@@ -85,6 +89,7 @@ public int read(byte[] b, int off, int len) throws IOException {
     @Override
     public void close() throws IOException {
         bytes = null;
+        position = -1;
     }
 
     @Override

src/test/java/htsjdk/samtools/seekablestream/ByteArraySeekableStreamTest.java

@@ -0,0 +1,116 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2017 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ */
+
+package htsjdk.samtools.seekablestream;
+
+import htsjdk.HtsjdkTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+
+/**
+ * Created by farjoun on 5/27/17.
+ */
+public class ByteArraySeekableStreamTest extends HtsjdkTest {
+    private final byte[] bytes = "ABCDE12345".getBytes();
+
+    @Test
+    public void testNormalBehavior() throws IOException {
+        ByteArraySeekableStream byteArraySeekableStream = new ByteArraySeekableStream(bytes);
+
+        Assert.assertEquals(byteArraySeekableStream.length(), 10);
+        for (int i = 0; i < 10; i++) {
+            Assert.assertFalse(byteArraySeekableStream.eof());
+            Assert.assertEquals(byteArraySeekableStream.position(), i);
+            Assert.assertEquals(byteArraySeekableStream.read(), bytes[i]);
+        }
+
+        Assert.assertTrue(byteArraySeekableStream.eof());
+        Assert.assertEquals(byteArraySeekableStream.position(), 10);
+        Assert.assertEquals(byteArraySeekableStream.read(), -1);
+
+        final long i = 0;
+        byteArraySeekableStream.seek(i);
+
+        Assert.assertEquals(byteArraySeekableStream.position(), i);
+        Assert.assertEquals(byteArraySeekableStream.read(), bytes[(int) i]);
+
+        byte[] copy = new byte[10];
+
+        Assert.assertEquals(byteArraySeekableStream.read(copy), 9);
+        Assert.assertEquals(byteArraySeekableStream.position(), 10);
+
+        byteArraySeekableStream.seek(0L);
+
+        Assert.assertEquals(byteArraySeekableStream.read(copy), 10);
+        Assert.assertEquals(byteArraySeekableStream.position(), 10);
+
+        Assert.assertEquals(copy, bytes);
+    }
+
+    @Test(expectedExceptions = IllegalArgumentException.class)
+    public void testCantSeekNegative() throws IOException {
+
+        ByteArraySeekableStream byteArraySeekableStream = new ByteArraySeekableStream(bytes);
+
+        byteArraySeekableStream.seek(-1L);
+
+        // if allowed to seek, this will throw OutOfBounds
+        final int f = byteArraySeekableStream.read();
+    }
+
+    @Test
+    public void testCantReadPostEof() throws IOException {
+
+        ByteArraySeekableStream byteArraySeekableStream = new ByteArraySeekableStream(bytes);
+        byte[] copy = new byte[10];
+
+        byteArraySeekableStream.seek(10);
+        Assert.assertEquals(byteArraySeekableStream.read(copy), -1);
+        Assert.assertEquals(byteArraySeekableStream.read(), -1);
+    }
+
+    @DataProvider(name = "abnormalReadRequests")
+    public Object[][] abnormalReadRequestsProvider() {
+        return new Object[][]{
+                {new byte[10], -1, 0},
+                {new byte[10], -1, -1},
+                {new byte[10], 0, -1},
+                {new byte[10], 0, -1},
+                {new byte[10], 0, 11},
+                {new byte[10], 6, 6},
+                {new byte[10], 11, 0},
+        };
+    }
+
+    @Test(dataProvider = "abnormalReadRequests", expectedExceptions = IndexOutOfBoundsException.class)
+    public void testAbnormalReadRequest(final byte[] b, final int off, final int length) throws IOException {
+
+        ByteArraySeekableStream byteArraySeekableStream = new ByteArraySeekableStream(bytes);
+        int i = byteArraySeekableStream.read(b, off, length);
+
+        Assert.assertEquals(i, -2); ///impossible
+    }
+}

src/test/java/htsjdk/samtools/sra/AbstractSRATest.java

@@ -25,14 +25,14 @@ public final void checkIfCanResolve() {
         canResolveNetworkAccession = SRAAccession.isValid(checkAccession);
     }
 
-    @BeforeMethod
+    @BeforeMethod(groups = "sra")
     public final void assertSRAIsSupported() {
         if(SRAAccession.checkIfInitialized() != null){
             throw new SkipException("Skipping SRA Test because SRA native code is unavailable.");
         }
     }
 
-    @BeforeMethod
+    @BeforeMethod(groups = "sra")
     public final void skipIfCantResolve(Method method, Object[] params) {
         String accession = null;