planemo print a warning when combined with --download_outputs and a workflow file

[Smeds]

I receive a warning when running planemo run --download_outputs with a workflow file, but not when using a workflow ID.

job file

QUERY_Sequence:
  class: File
  location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/GCF_000008865.2_ASM886v2_genomic.fna.gz
TARGET_Sequence:
  class: File
  location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz

Workflow file
https://github.com/galaxyproject/alignment-pipeline/blob/main/workflows/align_chain_net/align_chain_net.ga

Command and output

No Warning

planemo run cc50487d7a6e275a job_file.xml --profile vgp --output_json task.json --history_name MyAnalysis1
╭───────────────────────────────────────────────────────────────────────────────── Invocation <7544b591be7c303b> ──────────────────────────────────────────────────────────────────────────────────╮
│ Steps ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 17/17 scheduled                                                                                                                        │
│ Jobs  ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 15/15 terminal                                                                                                                         │
│ Job States ◆ 🟢 15 ◆                                                                                                                                                                             │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Run completed successfully.
None
All 1 test(s) executed passed.
gxid://workflows/cc50487d7a6e275a: passed

No Warning Note No warning when we run with workflow file without --download_options

planemo run align_chain_net.ga job_file.xml --profile vgp --output_json task.json --history_name MyAnalysis1
╭───────────────────────────────────────────────────────────────────────────────────────────────────────────── Invocation <f936f1821534054c> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Steps ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 17/17 scheduled                                                                                                                                                                               │
│ Jobs  ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 15/15 terminal                                                                                                                                                                                │
│ Job States ◆ 🟢 15 ◆                                                                                                                                                                                                                                    │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Run completed successfully.
None
All 1 test(s) executed passed.
align_chain_net.ga: passed

Warning

planemo run align_chain_net.ga job_file.xml --profile vgp --output_json task.json --download_outputs --output_directory result_data --history_name MyAnalysis1
╭───────────────────────────────────────────────────────────────────────────────── Invocation <29a454e0c483ea1d> ──────────────────────────────────────────────────────────────────────────────────╮
│ Steps ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 17/17 scheduled                                                                                                                        │
│ Jobs  ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 15/15 terminal                                                                                                                         │
│ Job States ◆ 🟢 15 ◆                                                                                                                                                                             │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
collecting outputs to directory /home/pks5769/temp/test_planemo_20250826/result_data
urllib3.connection WARNING: Failed to parse headers (url=https://vgp.usegalaxy.org:443/api/histories/bbd44e69cb8906b5d80b8c9977469838/contents/f9cad7b01a4721351ebc1ba292ebce13/display): [NoBoundaryInMultipartDefect()], unparsed data: ''
Traceback (most recent call last):
  File "/home/pks5769/temp/test_planemo_20250826/venv/lib/python3.9/site-packages/urllib3/connection.py", line 568, in getresponse
    assert_header_parsing(httplib_response.msg)
  File "/home/pks5769/temp/test_planemo_20250826/venv/lib/python3.9/site-packages/urllib3/util/response.py", line 88, in assert_header_parsing
    raise HeaderParsingError(defects=defects, unparsed_data=unparsed_data)
urllib3.exceptions.HeaderParsingError: [NoBoundaryInMultipartDefect()], unparsed data: ''
Run completed successfully.
None
All 1 test(s) executed passed.
align_chain_net.ga: passed

Used workflow ID belongs to the one we uploaded when running the first command

[mvdbeek]

I assume you've tried this more than once? The error message is about the response header ... even if planemo was doing faulty requests we're not expecting malformed response headers.

[mvdbeek]

Did everything else work out alright? This was likely handled by the retry setting in bioblend, in which case I would close this.

[Smeds]

@mvdbeek I’ve tested it several times and everything works, the workflow runs successfully and I receive the files, although with a warning. I also see the same warning when using planemo invocation_download, but the files are still downloaded from the invocation.

planemo invocation_download b3f68d6489236100 --output_directory result --profile vgp 
╭───────────────────────────────────────────────────────────────────────────────────────────────────────────── Invocation <b3f68d6489236100> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Steps ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 17/17 scheduled                                                                                                                                                                               │
│ Jobs  ◆ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ◆ 100% ◆ 15/15 terminal                                                                                                                                                                                │
│ Job States ◆ 🟢 15 ◆                                                                                                                                                                                                                                    │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
collecting outputs to directory /home/pks5769/temp/test_planemo_20250826/result
urllib3.connection WARNING: Failed to parse headers (url=https://vgp.usegalaxy.org:443/api/histories/bbd44e69cb8906b50f8685eb91814871/contents/f9cad7b01a472135a99c0c7fd8473ab3/display): [NoBoundaryInMultipartDefect()], unparsed data: ''
Traceback (most recent call last):
  File "/home/pks5769/temp/test_planemo_20250826/venv/lib/python3.9/site-packages/urllib3/connection.py", line 568, in getresponse
    assert_header_parsing(httplib_response.msg)
  File "/home/pks5769/temp/test_planemo_20250826/venv/lib/python3.9/site-packages/urllib3/util/response.py", line 88, in assert_header_parsing
    raise HeaderParsingError(defects=defects, unparsed_data=unparsed_data)
urllib3.exceptions.HeaderParsingError: [NoBoundaryInMultipartDefect()], unparsed data: ''