Pandoc failures can lead to report failures #799

effigies · 2023-04-14T18:49:47Z

What happened?

If pandoc fails to fully convert the Markdown boilerplate, our report compilation can fail here:

Lines 404 to 408 in 065c2b6

    
           text = ( 
        
               re.compile("<body>(.*?)</body>", re.DOTALL | re.IGNORECASE) 
        
               .findall((logs_path / "CITATION.html").read_text())[0] 
        
               .strip() 
        
           )

We should code a bit more defensively and allow for regexes to fail.

What command did you use?

Not given

What version of the software are you running?

22.1.1

How are you running this software?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

230413-04:06:39,364 nipype.workflow IMPORTANT:
        fMRIPrep finished successfully!
230413-04:06:39,364 nipype.workflow IMPORTANT:
        Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/fmriprep/logs/CITATION.md.", "stderr": "You are using fMRIPrep-22.1.1, and a newer version of fMRIPrep is available: 23.0.1.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
--topup-max-vols input is no longer used and the flag will be removed in a future release.
Could not generate CITATION.html file:
pandoc -s --bibliography /out/fmriprep/logs/CITATION.bib --citeproc --metadata pagetitle="fMRIPrep citation boilerplate" /out/fmriprep/logs/CITATION.md -o /out/fmriprep/logs/CITATION.html
Traceback (most recent call last):
  File "/opt/conda/bin/fmriprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/run.py", line 213, in main
    failed_reports = generate_reports(
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/reports/core.py", line 96, in generate_reports
    report_errors = [
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/reports/core.py", line 97, in <listcomp>
    run_reports(
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/reports/core.py", line 79, in run_reports
    return Report(
  File "/opt/conda/lib/python3.9/site-packages/niworkflows/reports/core.py", line 389, in generate_report
    re.compile("<body>(.*?)</body>", re.DOTALL | re.IGNORECASE)
IndexError: list index out of range

Additional information / screenshots

No response

effigies added the bug label Apr 14, 2023

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Pandoc failures can lead to report failures #799

Pandoc failures can lead to report failures #799

effigies commented Apr 14, 2023

Pandoc failures can lead to report failures #799

Pandoc failures can lead to report failures #799

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effigies commented Apr 14, 2023

What happened?

What command did you use?

What version of the software are you running?

How are you running this software?

Is your data BIDS valid?

Are you reusing any previously computed results?

Please copy and paste any relevant log output.

Additional information / screenshots