Redun¶
Here, we’ll see how to track redun workflow runs with LaminDB.
Note
This use case is based on github.com/ricomnl/bioinformatics-pipeline-tutorial.
# pip install lamindb redun git+http://github.com/laminlabs/redun-lamin-fasta
!lamin init --storage ./test-redun-lamin
Show code cell output
→ initialized lamindb: testuser1/test-redun-lamin
Amend the workflow¶
import lamindb as ln
import json
Show code cell output
→ connected lamindb: testuser1/test-redun-lamin
Let’s amend a redun workflow.py to register input & output artifacts in LaminDB:
To track the workflow run in LaminDB, add (see on GitHub):
ln.track(params=params)
To register the output file via LaminDB, add (see on GitHub):
ln.Artifact(output_path, description="results").save()
Run redun¶
Let’s see what the input files are:
!ls ./fasta
Show code cell output
KLF4.fasta MYC.fasta PO5F1.fasta SOX2.fasta
And call the workflow:
!redun run workflow.py main --input-dir ./fasta --tag run=test-run 1> run_logs.txt 2>run_logs.txt
Inspect the logs:
!cat run_logs.txt
Show code cell output
→ connected lamindb: testuser1/test-redun-lamin
→ created Transform('d3RZPwgr3JX90000'), started new Run('wIflPTUI...') at 2025-08-12 07:38:34 UTC
→ params: input_dir=./fasta, amino_acid=C, enzyme_regex=[KR], missed_cleavages=0, min_length=4, max_length=75, executor=Executor.default
• recommendation: to identify the script across renames, pass the uid: ln.track("d3RZPwgr3JX9", params={...})
! folder i[redun] Run Job 5b4ec09d: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/w2l5EFbBvq0Bd1DD0000.fasta, hash=d4a3f4fd), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, mFile(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=955adfee)
task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/Cv4Ij793VIUrcER10000.fasta, hash=3eab2bc8), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 472e10a4: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/UhoNfiLJnXSPG2A60000.fasta, hash=e17dc2cd), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 7233e2af: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/IW2fPn0oVZi5d3lc0000.fasta, hash=a121b9ac), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 3d6e7f16: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/w2l5EFbBvq0Bd1DD0000.fasta, hash=d4a3f4fd), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w2l5EFbBvq0Bd1DD0000.peptides.txt, hash=fa701c7b), amino_acid='C') on default
[redun] Run Job 7c87d702: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/Cv4Ij793VIUrcER10000.fasta, hash=3eab2bc8), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/Cv4Ij793VIUrcER10000.peptides.txt, hash=7d9c0404), amino_acid='C') on default
[redun] Run Job eb2c1631: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/UhoNfiLJnXSPG2A60000.fasta, hash=e17dc2cd), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/UhoNfiLJnXSPG2A60000.peptides.txt, hash=0a67d9c5), amino_acid='C') on default
[redun] Run Job de5742e9: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/IW2fPn0oVZi5d3lc0000.fasta, hash=a121b9ac), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/IW2fPn0oVZi5d3lc0000.peptides.txt, hash=65ff6272), amino_acid='C') on default
[redun] Run Job dfe618d9: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w2l5EFbBvq0Bd1DD0000.count.tsv, hash=ab87286b)) on default
[redun] Run Job d7d91c87: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/Cv4Ij793VIUrcER10000.count.tsv, hash=569d31f9)) on default
[redun] Run Job 5e9ebe99: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/UhoNfiLJnXSPG2A60000.count.tsv, hash=6797c1ac)) on default
[redun] Run Job ec55efcc: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/IW2fPn0oVZi5d3lc0000.count.tsv, hash=df8c1978)) on default
[redun] Run Job 9172feb5: bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w2l5EFbBvq0Bd1DD0000.count.tsv, hash=ab87286b), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run Job 55fc3ecf: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w2l5EFbBvq0Bd1DD0000.plot.png, hash=27cde5c3), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/protein_report.tsv, hash=2bad0113)) on default
INFO redun:scheduler.py:log()- Run Job 55fc3ecf: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w2l5EFbBvq0Bd1DD0000.plot.png, hash=27cde5c3), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/protein_report.tsv, hash=2bad0113)) on default
[redun] Run Job 1f92e3de: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=955adfee)) on default
INFO redun:scheduler.py:log()- Run Job 1f92e3de: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=955adfee)) on default
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1301, in log_job_statuses
self.log()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] | JOB STATUS 2025/08/12 07:38:51
INFO redun:scheduler.py:log()- | JOB STATUS 2025/08/12 07:38:51
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| JOB STATUS 2025/08/12 07:38:51'
Arguments: ()
[redun] | TASK PENDING RUNNING FAILED CACHED DONE TOTAL
INFO redun:scheduler.py:log()- | TASK PENDING RUNNING FAILED CACHED DONE TOTAL
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| TASK PENDING RUNNING FAILED CACHED DONE TOTAL'
Arguments: ()
[redun] |
INFO redun:scheduler.py:log()- |
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| '
Arguments: ()
[redun] | ALL 0 0 0 0 16 16
INFO redun:scheduler.py:log()- | ALL 0 0 0 0 16 16
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| ALL 0 0 0 0 16 16'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4'
Arguments: ()
[redun] | redun_lamin_fasta.finish 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | redun_lamin_fasta.finish 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| redun_lamin_fasta.finish 0 0 0 0 1 1'
Arguments: ()
[redun] | redun_lamin_fasta.main 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | redun_lamin_fasta.main 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: '| redun_lamin_fasta.main 0 0 0 0 1 1'
Arguments: ()
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1303, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1078, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1282, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1304, in log_job_statuses
self.log()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] Execution duration: 17.04 seconds
INFO redun:scheduler.py:log()- Execution duration: 17.04 seconds
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1618, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1164, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1082, in _run
self.log(f"Execution duration: {duration:.2f} seconds")
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1028, in log
self.logger.log(level, (" " * indent) + line)
Message: 'Execution duration: 17.04 seconds'
Arguments: ()
View data lineage:
artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()
Show code cell output
Track the redun execution id¶
If we want to be able to query LaminDB for redun execution ID, this here is a way to get it:
# export the run information from redun
!redun log --exec --exec-tag run=test-run --format json --no-pager > redun_exec.json
# load the redun execution id from the JSON and store it in the LaminDB run record
with open("redun_exec.json") as file:
redun_exec = json.loads(file.readline())
artifact.run.reference = redun_exec["id"]
artifact.run.reference_type = "redun_id"
artifact.run.save()
Run(uid='wIflPTUIEesAyTiy', started_at=2025-08-12 07:38:34 UTC, finished_at=2025-08-12 07:38:51 UTC, reference='ffce7fa5-39c6-4cd0-97d5-1c54deef977e', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=7, environment_id=1, created_by_id=1, created_at=2025-08-12 07:38:34 UTC)
Track the redun run report¶
Attach a run report:
report = ln.Artifact(
"run_logs.txt",
description=f"Redun run report of {redun_exec['id']}",
run=False,
visibility=0,
).save()
artifact.run.report = report
artifact.run.save()
Run(uid='wIflPTUIEesAyTiy', started_at=2025-08-12 07:38:34 UTC, finished_at=2025-08-12 07:38:51 UTC, reference='ffce7fa5-39c6-4cd0-97d5-1c54deef977e', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=8, environment_id=1, created_by_id=1, created_at=2025-08-12 07:38:34 UTC)
View transforms and runs in LaminHub¶
View the database content¶
ln.view()
Show code cell output
Artifact
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 8 | xhhF1o4jIgfew3BI0000 | None | Redun run report of ffce7fa5-39c6-4cd0-97d5-1c... | .txt | None | None | 33584 | kWLeBrPgSo05bxaJaq6KYQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-08-12 07:38:56.869000+00:00 | 1 | {'af': {'0': True}} | 1 |
| 6 | gDfCvw5KerS1jp1s0000 | data/results.tgz | None | .tgz | None | None | 68462 | pbnJlr7WfZA4EJI2DJlT_A | None | None | md5 | False | False | 1 | 1 | None | None | True | 1.0 | 2025-08-12 07:38:51.540000+00:00 | 1 | None | 1 |
| 4 | UhoNfiLJnXSPG2A60000 | fasta/PO5F1.fasta | None | .fasta | None | None | 477 | -7iJgveFO9ia0wE1bqVu6g | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-08-12 07:38:37.898000+00:00 | 1 | {'af': {'0': True}} | 1 |
| 5 | IW2fPn0oVZi5d3lc0000 | fasta/MYC.fasta | None | .fasta | None | None | 536 | WGbEtzPw-3bQEGcngO_pHQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-08-12 07:38:37.898000+00:00 | 1 | {'af': {'0': True}} | 1 |
| 3 | Cv4Ij793VIUrcER10000 | fasta/KLF4.fasta | None | .fasta | None | None | 609 | LyuoYkWs4SgYcH7P7JLJtA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-08-12 07:38:37.897000+00:00 | 1 | {'af': {'0': True}} | 1 |
| 2 | w2l5EFbBvq0Bd1DD0000 | fasta/SOX2.fasta | None | .fasta | None | None | 414 | C5q_yaFXGk4SAEpfdqBwnQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-08-12 07:38:37.896000+00:00 | 1 | {'af': {'0': True}} | 1 |
Feature
| uid | name | dtype | is_type | unit | description | array_rank | array_size | array_shape | proxy_dtype | synonyms | _expect_many | _curation | space_id | type_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||||
| 1 | 6mgb4IzJal9W | input_dir | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 2 | JcSfTQHhWtp6 | amino_acid | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 3 | 6YKqC0obIqSs | enzyme_regex | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 4 | yC8ZhV27jFE8 | missed_cleavages | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 5 | hVnH1AXb4gdl | min_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 6 | QaaVKOSHGsQG | max_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 7 | KXv8cvEb4rg6 | executor | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-08-12 07:38:34.903000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
FeatureValue
| value | hash | space_id | feature_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | ./fasta | G8diGhDfCu78R1WbXfsHOw | 1 | 1 | None | 2025-08-12 07:38:34.939000+00:00 | 1 | None | 1 |
| 2 | C | DWH4NwytHUEvgLhNFD4SVw | 1 | 2 | None | 2025-08-12 07:38:34.941000+00:00 | 1 | None | 1 |
| 3 | [KR] | zPuapwAPylpfWRQFOTw9Cg | 1 | 3 | None | 2025-08-12 07:38:34.943000+00:00 | 1 | None | 1 |
| 4 | 0 | z80ghJXVZe9m59_5-Ydk2g | 1 | 4 | None | 2025-08-12 07:38:34.945000+00:00 | 1 | None | 1 |
| 5 | 4 | qH_2eaLz5x2RgaZ7dUISLA | 1 | 5 | None | 2025-08-12 07:38:34.947000+00:00 | 1 | None | 1 |
| 6 | 75 | 0Jv0FUSjNlpGyQd-u141ww | 1 | 6 | None | 2025-08-12 07:38:34.949000+00:00 | 1 | None | 1 |
| 7 | Executor.default | BaNJiQQLvaFrvOtdglHU7w | 1 | 7 | None | 2025-08-12 07:38:34.951000+00:00 | 1 | None | 1 |
Run
| uid | name | started_at | finished_at | reference | reference_type | _is_consecutive | _status_code | space_id | transform_id | report_id | _logfile_id | environment_id | initiated_by_run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | wIflPTUIEesAyTiy | None | 2025-08-12 07:38:34.920500+00:00 | 2025-08-12 07:38:51.591301+00:00 | ffce7fa5-39c6-4cd0-97d5-1c54deef977e | redun_id | True | 0 | 1 | 1 | 8 | None | 1 | None | 2025-08-12 07:38:34.921000+00:00 | 1 | None | 1 |
Storage
| uid | root | description | type | region | instance_uid | space_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | pbFSTbEKaLl7 | /home/runner/work/redun-lamin/redun-lamin/docs... | None | local | None | iQlBPgD8uaqR | 1 | None | 2025-08-12 07:38:13.228000+00:00 | 1 | None | 1 |
Transform
| uid | key | description | type | source_code | hash | reference | reference_type | space_id | _template_id | version | is_latest | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||
| 1 | d3RZPwgr3JX90000 | workflow.py | workflow.py | script | """workflow.py."""\n\n# This code is a copy fr... | mHyxrE622q2fluxICu4XDw | None | None | 1 | None | None | True | 2025-08-12 07:38:34.918000+00:00 | 1 | None | 1 |
Delete the test instance:
Show code cell content
!rm -rf test-redun-lamin
!lamin delete --force test-redun-lamin
• deleting instance testuser1/test-redun-lamin