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bugfix/skewed-sample-hierarchy #450

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merged 3 commits into from
Oct 9, 2023
Merged

bugfix/skewed-sample-hierarchy #450

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bf44b1e
add patch for skewed sample hierarchy/additional samples
bgunnar5 Oct 9, 2023
4ee6d2e
update changelog
bgunnar5 Oct 9, 2023
7276c21
catch narrower range of exceptions
bgunnar5 Oct 9, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed
- A bug where the filenames in iterative workflows kept appending `.out`, `.partial`, or `.expanded` to the filenames stored in the `merlin_info/` subdirectory
- A bug where a skewed sample hierarchy was created when a restart was necessary in the `add_merlin_expanded_chain_to_chord` task

## [1.10.3]
### Added
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48 changes: 27 additions & 21 deletions merlin/common/tasks.py
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Expand Up @@ -298,27 +298,33 @@ def add_merlin_expanded_chain_to_chord( # pylint: disable=R0913,R0914
LOG.debug("chain added to chord")
else:
# recurse down the sample_index hierarchy
LOG.debug("recursing down sample_index hierarchy")
for next_index in sample_index.children.values():
next_index.name = os.path.join(sample_index.name, next_index.name)
LOG.debug("generating next step")
next_step = add_merlin_expanded_chain_to_chord.s(
task_type,
chain_,
samples[next_index.min - min_sample_id : next_index.max - min_sample_id],
labels,
next_index,
adapter_config,
next_index.min,
)
next_step.set(queue=chain_[0].get_task_queue())
LOG.debug(f"recursing with range {next_index.min}:{next_index.max}, {next_index.name} {signature(next_step)}")
LOG.debug(f"queuing samples[{next_index.min}:{next_index.max}] in for {chain_} in {next_index.name}...")
if self.request.is_eager:
next_step.delay()
else:
self.add_to_chord(next_step, lazy=False)
LOG.debug(f"queued for samples[{next_index.min}:{next_index.max}] in for {chain_} in {next_index.name}")
try:
LOG.debug("recursing down sample_index hierarchy")
for next_index in sample_index.children.values():
next_index_name_before = next_index.name
next_index.name = os.path.join(sample_index.name, next_index.name)
LOG.debug("generating next step")
next_step = add_merlin_expanded_chain_to_chord.s(
task_type,
chain_,
samples[next_index.min - min_sample_id : next_index.max - min_sample_id],
labels,
next_index,
adapter_config,
next_index.min,
)
next_step.set(queue=chain_[0].get_task_queue())
LOG.debug(f"recursing with range {next_index.min}:{next_index.max}, {next_index.name} {signature(next_step)}")
LOG.debug(f"queuing samples[{next_index.min}:{next_index.max}] in for {chain_} in {next_index.name}...")
if self.request.is_eager:
next_step.delay()
else:
self.add_to_chord(next_step, lazy=False)
LOG.debug(f"queued for samples[{next_index.min}:{next_index.max}] in for {chain_} in {next_index.name}")
except Exception as e:
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# Reset the index to what it was before so we don't accidentally create a bunch of extra samples upon restart
next_index.name = next_index_name_before
raise e

return ReturnCode.OK

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