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Stop AsyncBufferedIterator's thread on close even if its interrupt is swallowed - #1945
AsyncBufferedIterator.close() could hang forever when the iterator it wraps swallows the interrupt; it now also stops the background thread with a flag.
close() sets a volatile stopped flag before interrupting, and the background thread checks it after each read, so it stops even when the wrapped iterator catches the interrupt, clears it and throws something else, as AsyncBlockCompressedInputStream does.
The new test wraps an iterator that does exactly that and runs close() on a daemon thread, failing instead of hanging if close() doesn't return.
Fixed an issue where closing an asynchronous buffered iterator could hang indefinitely if the underlying iterator ignored thread interrupts. Closing now completes without waiting for that iterator to respond, making shutdown more reliable.
… swallowed
close() stopped the background thread only by interrupting it. An
iterator that catches the interrupt, clears it and throws something
else, as AsyncBlockCompressedInputStream does while it waits for a
read-ahead block, made the thread queue that exception as a read
failure and read on until the queue was full, so put() and then
close()'s join() waited forever.
close() now sets a volatile flag before it interrupts, and the thread
checks it after each read. Setting it first means that a thread which
has seen the interrupt also sees the flag, and one that checked the
flag before close() still has the interrupt pending, so its put()
throws rather than blocks.
AsyncBufferedIterator.close() now sets a stop flag before interrupting its background thread. The read loop checks the flag after reads and exits even when the wrapped iterator clears the interrupt. A regression test covers this case.
Changes: AsyncBufferedIterator shutdown
Layer / File(s)
Summary
Stop signal and background exit src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java
close() sets a volatile stop flag before interrupting the background thread. readAhead() and backgroundRun() check the flag and stop reading without enqueuing another block.
Shutdown regression test and release note src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java, CHANGELOG.md
A test verifies that close() completes when the wrapped iterator swallows an interrupt. The changelog records the fix in the 6.0.1 patch release.
samtools/htsjdk#1943: Addresses failure handling in AsyncBlockCompressedInputStream, a related asynchronous BGZF read path.
Merge Risk: Low · previous review 50c01
This change stops close() from hanging when the wrapped iterator swallows an interrupt and then throws. A hang remains possible if the iterator instead returns a record and its next hasNext() blocks. That case is narrow and was already present, so merging is low risk; checking the stop flag right after next() would close it.
Pre-merge checks: 4 · 1
Failed checks: 1 warning
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Docstring Coverage
Docstring coverage is 40.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documenta…
Write docstrings for the functions missing them to satisfy the coverage threshold.
Passed checks: 4 passed
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Description Check
Check skipped - CodeRabbit’s high-level summary is enabled.
Title check
The title names the main change: AsyncBufferedIterator's background thread now stops on close() even when the wrapped iterator swallows the interrupt. The raw summary and PR objectives both describe a…
Linked Issues check
The PR meets the coding requirements in issue #1944. AsyncBufferedIterator.close() sets the volatile stopped flag before interrupting and joining the background thread. readAhead() checks the fl…
Out of Scope Changes check
The changes stay within issue #1944. The production change stops the background thread during close, the test covers the interrupt-swallowing case, and the changelog entry documents the fix. No unrela…
Full details: Title check
Explanation
The title names the main change: AsyncBufferedIterator's background thread now stops on close() even when the wrapped iterator swallows the interrupt. The raw summary and PR objectives both describe a volatile stop flag, checked after each read, that makes this happen. The title is specific, concise, and matches the changeset.
Full details: Linked Issues check
Explanation
The PR meets the coding requirements in issue #1944. AsyncBufferedIterator.close() sets the volatile stopped flag before interrupting and joining the background thread. readAhead() checks the flag during reads, and backgroundRun() checks it before queue insertion. The new test uses an iterator that swallows the interrupt and verifies that close() returns within a timeout.
Full details: Out of Scope Changes check
Explanation
The changes stay within issue #1944. The production change stops the background thread during close, the test covers the interrupt-swallowing case, and the changelog entry documents the fix. No unrelated change is shown.
Full details: Docstring Coverage
Explanation
Docstring coverage is 40.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 5 functions across 2 files. (1 skipped: 1 unsupported.)
Resolution
Write docstrings for the functions missing them to satisfy the coverage threshold.
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Actionable comments posted: 1
🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at
@src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java:
- Line 210: Update the AsyncBufferedIterator producer loop to check the stopped
flag immediately after next() returns and before calling
underlyingIterator.hasNext() again, so shutdown does not enter another
potentially blocking read.
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AsyncBufferedIterator.close()could hang forever when the iterator it wraps swallows the interrupt; it now also stops the background thread with a flag.close()sets a volatilestoppedflag before interrupting, and the background thread checks it after each read, so it stops even when the wrapped iterator catches the interrupt, clears it and throws something else, asAsyncBlockCompressedInputStreamdoes.close()on a daemon thread, failing instead of hanging ifclose()doesn't return.Found while reading broadinstitute/picard#2063, which reported 3 hangs in 1,000 closes.
Fixes #1944
Summary by CodeRabbit