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Update for to use Java 21 #1698

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Update for to use Java 21 #1698

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0895474
Update for to use Java 21
lbergelson Dec 18, 2023
3426875
updating to spotbugs 6.0.3
lbergelson Dec 18, 2023
12d8d50
set back to high confidence only
lbergelson Dec 19, 2023
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14 changes: 7 additions & 7 deletions .github/workflows/tests.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
java: [ 17 ]
java: [ 21 ]
experimental: [false]
fail-fast: false
continue-on-error: ${{ matrix.experimental }}
Expand Down Expand Up @@ -49,10 +49,10 @@ jobs:
name: Tests that require external APIs
steps:
- uses: actions/checkout@v3
- name: Set up java 17
- name: Set up java 21
uses: actions/setup-java@v3
with:
java-version: '17'
java-version: '21'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
Expand All @@ -75,10 +75,10 @@ jobs:
name: FTP tests
steps:
- uses: actions/checkout@v3
- name: Set up java 17
- name: Set up java 21
uses: actions/setup-java@v3
with:
java-version: '17'
java-version: '21'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
Expand All @@ -100,10 +100,10 @@ jobs:
name: SpotBugs
steps:
- uses: actions/checkout@v3
- name: Set up java 17
- name: Set up java 21
uses: actions/setup-java@v3
with:
java-version: '17'
java-version: '21'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
Expand Down
7 changes: 4 additions & 3 deletions build.gradle
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Expand Up @@ -11,7 +11,7 @@ plugins {
id 'jacoco'
id 'com.palantir.git-version' version '0.11.0'
id 'com.github.johnrengelman.shadow' version '8.1.1'
id 'com.github.spotbugs' version "5.0.13"
id 'com.github.spotbugs' version "6.0.4"
}

repositories {
Expand Down Expand Up @@ -47,7 +47,7 @@ dependencies {

java {
toolchain {
languageVersion = JavaLanguageVersion.of(17)
languageVersion = JavaLanguageVersion.of(21)
}
withJavadocJar()
withSourcesJar()
Expand Down Expand Up @@ -174,7 +174,8 @@ if(project == rootProject) {
}

spotbugs {
reportLevel = 'high'
effort = com.github.spotbugs.snom.Effort.valueOf('MAX')
reportLevel = com.github.spotbugs.snom.Confidence.valueOf('HIGH')
excludeFilter = file('gradle/spotbugs-exclude.xml')
}

Expand Down
25 changes: 11 additions & 14 deletions src/main/java/htsjdk/samtools/util/DiskBackedQueue.java
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Expand Up @@ -54,7 +54,7 @@
*
* Created by bradt on 4/28/14.
*/
public class DiskBackedQueue<E> implements Queue<E> {
public class DiskBackedQueue<E> implements Queue<E>, AutoCloseable {
private final int maxRecordsInRamQueue;
private final Queue<E> ramRecords;
private Path diskRecords = null;
Expand Down Expand Up @@ -95,7 +95,7 @@ private DiskBackedQueue(final SortingCollection.Codec<E> codec,
this.tmpDirs = tmpDirs;
this.codec = codec;
this.maxRecordsInRamQueue = (maxRecordsInRam == 0) ? 0 : maxRecordsInRam - 1; // the first of our ram records is stored as headRecord
this.ramRecords = new ArrayDeque<E>(this.maxRecordsInRamQueue);
this.ramRecords = new ArrayDeque<>(this.maxRecordsInRamQueue);
}

/**
Expand Down Expand Up @@ -248,18 +248,6 @@ public void clear() {
this.canAdd = true;
}

/**
* Clean up disk resources in case clear() has not been explicitly called (as would be preferable)
* Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
*
* @throws Throwable
*/
@Override
protected void finalize() throws Throwable {
this.closeIOResources();
super.finalize(); // NB: intellij wanted me to do this. Need I? I'm not extending anything
}

/**
* Write the present record to the end of a file representing the tail of the queue.
* @throws RuntimeIOException
Expand Down Expand Up @@ -420,4 +408,13 @@ public Object[] toArray() {
public <T1> T1[] toArray(final T1[] a) {
throw new UnsupportedOperationException("DiskBackedQueue does not support toArray(T1[] a)");
}

/**
* Clean up disk resources in case clear() has not been explicitly called (as would be preferable)
* Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
*/
@Override
public void close() {
clear();
}
}
1 change: 0 additions & 1 deletion src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java
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Expand Up @@ -56,7 +56,6 @@ public OutputStream makeValue(final File file) {
// In case the file could not be opened because of too many file handles, try to force
// file handles to be closed.
System.gc();
System.runFinalization();
try {
return IOUtil.maybeBufferOutputStream(new FileOutputStream(file, true));
}
Expand Down
22 changes: 16 additions & 6 deletions src/main/java/htsjdk/samtools/util/SamRecordTrackingBuffer.java
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Expand Up @@ -54,7 +54,7 @@
*
* @author bradtaylor
*/
public class SamRecordTrackingBuffer<T extends SamRecordWithOrdinal> {
public class SamRecordTrackingBuffer<T extends SamRecordWithOrdinal> implements AutoCloseable {
private int availableRecordsInMemory; // how many more records can we store in memory
private final int blockSize; // the size of each block
private final List<File> tmpDirs; // the list of temporary directories to use
Expand All @@ -78,7 +78,7 @@ public SamRecordTrackingBuffer(final int maxRecordsInRam, final int blockSize, f
this.tmpDirs = tmpDirs;
this.queueHeadRecordIndex = -1;
this.queueTailRecordIndex = -1;
this.blocks = new ArrayDeque<BufferBlock>();
this.blocks = new ArrayDeque<>();
this.header = header;
this.clazz = clazz;
}
Expand Down Expand Up @@ -184,6 +184,7 @@ public void setResultState(final SamRecordWithOrdinal samRecordWithOrdinal, fina
/**
* Close IO resources associated with each underlying BufferBlock
*/
@Override
public void close() {
while (!blocks.isEmpty()) {
final BufferBlock block = blocks.pollFirst();
Expand All @@ -194,7 +195,7 @@ public void close() {
/**
* This stores blocks of records, either in memory or on disk, or both!
*/
private class BufferBlock {
private class BufferBlock implements AutoCloseable {
private final DiskBackedQueue<SAMRecord> recordsQueue;
private final int maxBlockSize;
private long currentStartIndex;
Expand Down Expand Up @@ -256,7 +257,7 @@ public void add(final SamRecordWithOrdinal samRecordWithOrdinal) {
}
}

private int ensureIndexFitsInAnInt(final long value) {
private static int ensureIndexFitsInAnInt(final long value) {
if (value < Integer.MIN_VALUE || Integer.MAX_VALUE < value) throw new SAMException("Error: index out of range: " + value);
return (int)value;
}
Expand Down Expand Up @@ -288,7 +289,7 @@ public SamRecordWithOrdinal next() throws IllegalStateException {
if (this.canEmit()) {
try {
// create a wrapped record for the head of the queue, and set the underlying record's examined information appropriately
final SamRecordWithOrdinal samRecordWithOrdinal = clazz.newInstance();
final SamRecordWithOrdinal samRecordWithOrdinal = clazz.getDeclaredConstructor().newInstance();
samRecordWithOrdinal.setRecord(this.recordsQueue.poll());
samRecordWithOrdinal.setRecordOrdinal(this.currentStartIndex);
samRecordWithOrdinal.setResultState(this.resultStateIndexes.get(ensureIndexFitsInAnInt(this.currentStartIndex - this.originalStartIndex)));
Expand Down Expand Up @@ -316,6 +317,15 @@ public SamRecordWithOrdinal next() throws IllegalStateException {
* Close disk IO resources associated with the underlying records queue.
* This must be called when a block is no longer needed in order to prevent memory leaks.
*/
public void clear() { this.recordsQueue.clear(); }
public void clear() { this.recordsQueue.close(); }

/**
* Close disk IO resources associated with the underlying records queue.
* This must be called when a block is no longer needed in order to prevent memory leaks.
*/
@Override
public void close() {
clear();
}
}
}
62 changes: 31 additions & 31 deletions src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
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Expand Up @@ -11,19 +11,19 @@ public class SAMBinaryTagAndValueUnitTest extends HtsjdkTest {
@DataProvider(name="allowedAttributeTypes")
public Object[][] allowedTypes() {
return new Object[][] {
{new String("a string")},
{new Byte((byte) 7)},
{new Short((short) 8)},
{new Integer(0)},
{new Character('C')},
{new Float(0.1F)},
{"a string"},
{Byte.valueOf((byte) 7)},
{Short.valueOf((short) 8)},
{Integer.valueOf(0)},
{Character.valueOf('C')},
{Float.valueOf(0.1F)},
// unsigned longs
{new Long(0)},
{new Long(BinaryCodec.MAX_UINT)},
{Long.valueOf(0)},
{Long.valueOf(BinaryCodec.MAX_UINT)},
// signed longs
{new Long(-1L)},
{new Long(Integer.MAX_VALUE)},
{new Long(Integer.MIN_VALUE)},
{Long.valueOf(-1L)},
{Long.valueOf(Integer.MAX_VALUE)},
{Long.valueOf(Integer.MIN_VALUE)},
// array values
{new byte[]{0, 1, 2}},
{new short[]{3, 4, 5}},
Expand All @@ -45,9 +45,9 @@ public void test_isAllowedConstructor(final Object value) {
@DataProvider(name="notAllowedAttributeTypes")
public Object[][] notAllowedTypes() {
return new Object[][] {
{new Long(BinaryCodec.MAX_UINT + 1L)},
{new Long(Integer.MIN_VALUE - 1L)},
{new Double(0.3F)},
{Long.valueOf(BinaryCodec.MAX_UINT + 1L)},
{Long.valueOf(Integer.MIN_VALUE - 1L)},
{Double.valueOf(0.3F)},
{new Object()},
{new Object[]{}},
{new Integer[]{}}
Expand Down Expand Up @@ -76,7 +76,7 @@ public Object[][] allowedUnsignedArrayTypes() {
@Test(dataProvider="allowedUnsignedArrayTypes")
public void test_isAllowedUnsignedArrayAttribute(final Object value) {
final short binaryTag = SAMTag.makeBinaryTag("UI");
Assert.assertNotNull(new SAMBinaryTagAndUnsignedArrayValue(binaryTag, value));
new SAMBinaryTagAndUnsignedArrayValue(binaryTag, value);
}

@DataProvider(name="notAllowedUnsignedArrayTypes")
Expand All @@ -97,29 +97,29 @@ public void test_isNotAllowedUnsignedArrayAttribute(final Object value) {
public Object[][] hashCopyEquals() {
final short tag = SAMTag.makeBinaryTag("UI");
return new Object[][] {
{new SAMBinaryTagAndValue(tag, new String("a string")), new SAMBinaryTagAndValue(tag, new String("a string")), true, true},
{new SAMBinaryTagAndValue(tag, new String("a string")), new SAMBinaryTagAndValue(tag, new String("different string")), false, false},
{new SAMBinaryTagAndValue(tag, "a string"), new SAMBinaryTagAndValue(tag, "a string"), true, true},
{new SAMBinaryTagAndValue(tag, "a string"), new SAMBinaryTagAndValue(tag, "different string"), false, false},

{new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
{new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
{new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), true, true},
{new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 0)), new SAMBinaryTagAndValue(tag, Byte.valueOf((byte) 1)), false, false},

{new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
{new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
{new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), true, true},
{new SAMBinaryTagAndValue(tag, Short.valueOf((short) 0)), new SAMBinaryTagAndValue(tag, Short.valueOf((short) 1)), false, false},

{new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
{new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
{new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), true, true},
{new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), new SAMBinaryTagAndValue(tag, Integer.valueOf(0)), true, true},

{new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
{new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
{new SAMBinaryTagAndValue(tag, Character.valueOf('C')), new SAMBinaryTagAndValue(tag, Character.valueOf('C')), true, true},
{new SAMBinaryTagAndValue(tag, Character.valueOf('C')), new SAMBinaryTagAndValue(tag, Character.valueOf('D')), false, false},

{new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
{new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
{new SAMBinaryTagAndValue(tag,Float.valueOf(0.1F)), new SAMBinaryTagAndValue(tag, Float.valueOf(0.1F)), true, true},
{new SAMBinaryTagAndValue(tag, Float.valueOf(0.1F)), new SAMBinaryTagAndValue(tag, Float.valueOf(0.2F)), false, false},

{new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
{new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
{new SAMBinaryTagAndValue(tag,Long.valueOf(37L)), new SAMBinaryTagAndValue(tag, Long.valueOf(37L)), true, true},
{new SAMBinaryTagAndValue(tag, Long.valueOf(37L)), new SAMBinaryTagAndValue(tag, Long.valueOf(38L)), false, false},

{new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
{new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
{new SAMBinaryTagAndValue(tag,Long.valueOf(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT)), true, true},
{new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, Long.valueOf(BinaryCodec.MAX_UINT-1)), false, false},

// arrays

Expand Down