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Fix missing sequencing_started status #19

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Merged
ssjunnebo merged 2 commits into from
Apr 24, 2026
Merged

Fix missing sequencing_started status #19

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f5576c9
Set sequencing_started if sequencing finished before sequencing_start…
ssjunnebo Apr 23, 2026
a1c289e
Update lockfile
ssjunnebo Apr 23, 2026
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4 changes: 4 additions & 0 deletions dataflow_transfer/dataflow_transfer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,10 @@ def process_run(run_dir, sequencer, config):
f"Run {run_dir} is already marked as sequenced, but transfer not complete. "
"Will attempt final transfer again."
)
if not run.has_status("sequencing_started"):
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@aanil aanil Apr 23, 2026

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What happens if final_sync_successful is already true but sequencing_started has not been set? Is that something that can happen?

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@ssjunnebo ssjunnebo Apr 23, 2026

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That shouldn't happen. run.final_sync_successful is only true if final_rsync_exitcode_file is 0, and that file is only generated if run.start_transfer(final=True) has been run, which only happens if line 48 is true (if not run.final_sync_successful:) which will now set sequencing_started.

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@aanil aanil Apr 23, 2026

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Sounds good!

run.update_statusdb(
status="sequencing_started"
) # Cover case where sequencing finished before sequencing_started was set (e.g. due to paused cronjob)
run.update_statusdb(status="sequencing_finished")
run.start_transfer(final=True)
return
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -20,7 +20,7 @@ ignore = [

[project]
name = "dataflow_transfer"
version = "1.1.4"
version = "1.1.5"
description = "Script for transferring sequencing data from sequencers to storage"
authors = [
{ name = "Sara Sjunnebo", email = "sara.sjunnebo@scilifelab.se" },
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2 changes: 1 addition & 1 deletion uv.lock
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