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

Hide code cell output

 initialized lamindb: testuser1/test-redun-lamin

Amend the workflow

import lamindb as ln
import json

Hide 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

Hide 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

Hide code cell output

 connected lamindb: testuser1/test-redun-lamin
 created Transform('voo6oVkh5yT30000'), started new Run('zOIKsc7W...') at 2025-07-14 06:39:55 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("voo6oVkh5yT3", params={...})
! folder i[redun] Run    Job c57c0173:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/gBPet3CnLnNv1Gv40000.fasta, hash=53d5ac53), 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=76aa4c31)
task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ANqOZxj9OBPwLmiH0000.fasta, hash=13ba1e26), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 41136ab3:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ClDisYKX6gsThIqi0000.fasta, hash=ca68ec0f), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 663f4d38:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2TPYJWEEx9xL4pmk0000.fasta, hash=051a8b4d), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 258ea312:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/gBPet3CnLnNv1Gv40000.fasta, hash=53d5ac53), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.peptides.txt, hash=4cd8b8e0), amino_acid='C') on default
[redun] Run    Job 77dc5189:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ANqOZxj9OBPwLmiH0000.fasta, hash=13ba1e26), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ANqOZxj9OBPwLmiH0000.peptides.txt, hash=2ae0c08a), amino_acid='C') on default
[redun] Run    Job cb5376dd:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ClDisYKX6gsThIqi0000.fasta, hash=ca68ec0f), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ClDisYKX6gsThIqi0000.peptides.txt, hash=60c26c47), amino_acid='C') on default
[redun] Run    Job d60fbcf0:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2TPYJWEEx9xL4pmk0000.fasta, hash=051a8b4d), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2TPYJWEEx9xL4pmk0000.peptides.txt, hash=4460e3cd), amino_acid='C') on default
[redun] Run    Job 8beb6e6d:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.count.tsv, hash=1ebc7bd0)) on default
[redun] Run    Job 91730592:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ANqOZxj9OBPwLmiH0000.count.tsv, hash=8a53cf32)) on default
[redun] Run    Job 6c0406df:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ClDisYKX6gsThIqi0000.count.tsv, hash=bb179599)) on default
[redun] Run    Job 0475dc37:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2TPYJWEEx9xL4pmk0000.count.tsv, hash=de5f1492)) on default
[redun] Run    Job 49063be5:  bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.count.tsv, hash=1ebc7bd0), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run    Job d30d05fb:  bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.plot.png, hash=fcbdcdb2), 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=98eea799)) on default
INFO	redun:scheduler.py:log()- Run    Job d30d05fb:  bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.plot.png, hash=fcbdcdb2), 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=98eea799)) on default
[redun] Run    Job 27b5d3d9:  redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=76aa4c31)) on default
INFO	redun:scheduler.py:log()- Run    Job 27b5d3d9:  redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=76aa4c31)) 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1272, in log_job_statuses
    self.log()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
    self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] | JOB STATUS 2025/07/14 06:40:10
INFO	redun:scheduler.py:log()- | JOB STATUS 2025/07/14 06:40:10
--- 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, in log
    self.logger.log(level, (" " * indent) + line)
Message: '| JOB STATUS 2025/07/14 06:40:10'
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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, 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 999, 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
    self._process_events(result)
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
    self.log_job_statuses()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1275, in log_job_statuses
    self.log()
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
    self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] Execution duration: 15.45 seconds
INFO	redun:scheduler.py:log()- Execution duration: 15.45 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 1620, in run_command
    result = scheduler.run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
    result: Promise[Result] = self._run(
  File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1053, 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 999, in log
    self.logger.log(level, (" " * indent) + line)
Message: 'Execution duration: 15.45 seconds'
Arguments: ()

View data lineage:

artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()

Hide code cell output

_images/4217da32fc63bc7328e81576685a36b56ef961d03464ce41c6aeace91a8bf72e.svg

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='zOIKsc7WptNvmIPd', started_at=2025-07-14 06:39:55 UTC, finished_at=2025-07-14 06:40:10 UTC, reference='7794a371-a39b-40b0-9ee1-06c45a50e45d', 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=2025-07-14 06:39:55 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='zOIKsc7WptNvmIPd', started_at=2025-07-14 06:39:55 UTC, finished_at=2025-07-14 06:40:10 UTC, reference='7794a371-a39b-40b0-9ee1-06c45a50e45d', 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=2025-07-14 06:39:55 UTC)

View transforms and runs in LaminHub

hub

View the database content

ln.view()

Hide 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 2ckt8FMNqL84ornJ0000 None Redun run report of 7794a371-a39b-40b0-9ee1-06... .txt None None 33569 AubZJGtTc4bhmSUmoj_1kA None None md5 True False 1 1 None None True NaN 2025-07-14 06:40:15.613000+00:00 1 {'af': {'0': True}} 1
6 1LcJM28b41qtSOPj0000 data/results.tgz None .tgz None None 68913 pMSTlgRpuF3rNTD6Yid6_A None None md5 False False 1 1 None None True 1.0 2025-07-14 06:40:10.367000+00:00 1 None 1
5 2TPYJWEEx9xL4pmk0000 fasta/PO5F1.fasta None .fasta None None 477 -7iJgveFO9ia0wE1bqVu6g None None md5 True False 1 1 None None True NaN 2025-07-14 06:39:58.241000+00:00 1 {'af': {'0': True}} 1
4 ClDisYKX6gsThIqi0000 fasta/MYC.fasta None .fasta None None 536 WGbEtzPw-3bQEGcngO_pHQ None None md5 True False 1 1 None None True NaN 2025-07-14 06:39:58.240000+00:00 1 {'af': {'0': True}} 1
3 ANqOZxj9OBPwLmiH0000 fasta/SOX2.fasta None .fasta None None 414 C5q_yaFXGk4SAEpfdqBwnQ None None md5 True False 1 1 None None True NaN 2025-07-14 06:39:58.239000+00:00 1 {'af': {'0': True}} 1
2 gBPet3CnLnNv1Gv40000 fasta/KLF4.fasta None .fasta None None 609 LyuoYkWs4SgYcH7P7JLJtA None None md5 True False 1 1 None None True NaN 2025-07-14 06:39:58.238000+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 PM8NrrmDTPsP input_dir str None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
2 XA1AraBxSLYg amino_acid str None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
3 yVLmzCgYgVg8 enzyme_regex str None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
4 nzp52r3kZ7H4 missed_cleavages int None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
5 WywWAMS203eT min_length int None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
6 WW7l2IClru86 max_length int None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+00:00 1 {'af': {'0': None, '1': True, '2': False}} 1
7 3b2SdqhLQprf executor str None None None 0 0 None None None None None 1 None None 2025-07-14 06:39:55.454000+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 2025-07-14 06:39:55.526000+00:00 1 None 1
2 C DWH4NwytHUEvgLhNFD4SVw 1 2 None 2025-07-14 06:39:55.531000+00:00 1 None 1
3 [KR] zPuapwAPylpfWRQFOTw9Cg 1 3 None 2025-07-14 06:39:55.536000+00:00 1 None 1
4 0 z80ghJXVZe9m59_5-Ydk2g 1 4 None 2025-07-14 06:39:55.540000+00:00 1 None 1
5 4 qH_2eaLz5x2RgaZ7dUISLA 1 5 None 2025-07-14 06:39:55.545000+00:00 1 None 1
6 75 0Jv0FUSjNlpGyQd-u141ww 1 6 None 2025-07-14 06:39:55.549000+00:00 1 None 1
7 Executor.default BaNJiQQLvaFrvOtdglHU7w 1 7 None 2025-07-14 06:39:55.554000+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 zOIKsc7WptNvmIPd None 2025-07-14 06:39:55.477549+00:00 2025-07-14 06:40:10.412039+00:00 7794a371-a39b-40b0-9ee1-06c45a50e45d redun_id True 0 1 1 8 None 1 None 2025-07-14 06:39:55.478000+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 p0dJWtdparDR /home/runner/work/redun-lamin/redun-lamin/docs... None local None iQlBPgD8uaqR 1 None 2025-07-14 06:39:36.614000+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 voo6oVkh5yT30000 workflow.py workflow.py script """workflow.py."""\n\n# This code is a copy fr... mHyxrE622q2fluxICu4XDw None None 1 None None True 2025-07-14 06:39:55.472000+00:00 1 None 1

Delete the test instance:

Hide code cell content

!rm -rf test-redun-lamin
!lamin delete --force test-redun-lamin
 deleting instance testuser1/test-redun-lamin