Skip to content

Error when paperbee merges duplications and the publication has no publication date #27

@javier-marchena-hurtado

Description

Describe the bug

When several databases (for example, biorxiv and PubMed) find the same paper (duplicate) and merge the duplicate, if the paper has no publication date, it leads to an error:

2025-07-21 16:07:01,380 INFO: Finding and merging duplications...
Traceback (most recent call last):
File "/home/javier/mambaforge/bin/paperbee", line 8, in
sys.exit(main())
File "/home/javier/mambaforge/lib/python3.10/site-packages/PaperBee/daily_posting.py", line 130, in main
papers, response_slack, response_telegram, response_zulip = asyncio.run(
File "/home/javier/mambaforge/lib/python3.10/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/home/javier/mambaforge/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
return future.result()
File "/home/javier/mambaforge/lib/python3.10/site-packages/PaperBee/daily_posting.py", line 85, in daily_papers_search
papers, response_slack, response_telegram, response_zulip = await finder.run_daily(
File "/home/javier/mambaforge/lib/python3.10/site-packages/PaperBee/papers/papers_finder.py", line 335, in run_daily
processed_articles = self.find_and_process_papers()
File "/home/javier/mambaforge/lib/python3.10/site-packages/PaperBee/papers/papers_finder.py", line 132, in find_and_process_papers
findpapers.search(
File "/home/javier/mambaforge/lib/python3.10/site-packages/findpapers/tools/search_runner_tool.py", line 557, in search
search.merge_duplications()
File "/home/javier/mambaforge/lib/python3.10/site-packages/findpapers/models/search.py", line 276, in merge_duplications
if (paper_1.publication_date is None or paper_2.publication_date is None) or
AttributeError: 'NoneType' object has no attribute 'publication_date'

To Reproduce

Steps to reproduce the behavior:

  1. Use the following query in the config.yml file:

query: "[CITE-seq] OR [single-cell in colorectal cancer] OR [variant effect prediction] OR [normalization in single-cell omics]"

  1. This error happened to me on 21st July, 2025 when running the command "paperbee post --config config.yml --interactive --since 20". So run this command, but adjusting the number of days (the --since parameter) to search back to at least 1st July, 2025.

Expected behavior

I expect paperbee to run normally and not give errors.

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions