Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Pubmed retractions #1428

Merged
merged 23 commits into from
Dec 31, 2023
Merged

Pubmed retractions #1428

merged 23 commits into from
Dec 31, 2023

Commits on Dec 13, 2023

  1. Increase random magnitude for retry_pause

    @kkaris
    kkaris committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    fee30b6 View commit details
    Browse the repository at this point in the history

  2. Add status code for retry

    @kkaris
    kkaris committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    aed52d8 View commit details
    Browse the repository at this point in the history

  3. Increase initial retry_pause time

    @kkaris
    kkaris committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    10a7f68 View commit details
    Browse the repository at this point in the history

Commits on Dec 14, 2023

  1. Add function to get publication types per PubmedArticle

    @kkaris
    kkaris committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    0440f23 View commit details
    Browse the repository at this point in the history

  2. Add code to generate retractions resource file

    @kkaris
    kkaris committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    5427359 View commit details
    Browse the repository at this point in the history

  3. Skip inner tqdm

    @kkaris
    kkaris committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    ca4bc05 View commit details
    Browse the repository at this point in the history

  4. Fix retraction matching string

    @kkaris
    kkaris committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    33ac85c View commit details
    Browse the repository at this point in the history

  5. Fix file ending

    @kkaris
    kkaris committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    8684ea0 View commit details
    Browse the repository at this point in the history

Commits on Dec 15, 2023

  1. Use csv to write retractions

    @kkaris
    kkaris committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    a8d36b9 View commit details
    Browse the repository at this point in the history

  2. Allow skipping download of files

    @kkaris
    kkaris committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    b0dc6cf View commit details
    Browse the repository at this point in the history

  3. Warn if no files or no retractions found

    @kkaris
    kkaris committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    9f059f3 View commit details
    Browse the repository at this point in the history

  4. Add resource file for retracted publications

    @kkaris
    kkaris committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    e767354 View commit details
    Browse the repository at this point in the history

  5. Add function to check if PMID is retracted

    @kkaris
    kkaris committed Dec 15, 2023
    Configuration menu
    Copy the full SHA
    2a13d10 View commit details
    Browse the repository at this point in the history

Commits on Dec 16, 2023

  1. Assume incoming pmid is string

    @kkaris
    kkaris committed Dec 16, 2023
    Configuration menu
    Copy the full SHA
    8445e6f View commit details
    Browse the repository at this point in the history

  2. Add retracted reading source filter in assemble_corpus.py

    @kkaris
    kkaris committed Dec 16, 2023
    Configuration menu
    Copy the full SHA
    c6816e7 View commit details
    Browse the repository at this point in the history

  3. Test new assemble_corpus function

    @kkaris
    kkaris committed Dec 16, 2023
    Configuration menu
    Copy the full SHA
    3d5aadb View commit details
    Browse the repository at this point in the history

  4. Move import to function to avoid global dependency

    @kkaris
    kkaris committed Dec 16, 2023
    Configuration menu
    Copy the full SHA
    18f89cd View commit details
    Browse the repository at this point in the history

Commits on Dec 18, 2023

  1. De-compress retractions and sort them numerically

    @kkaris
    kkaris committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    8df5a50 View commit details
    Browse the repository at this point in the history

  2. Decompress retractions file

    @kkaris
    kkaris committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    73807e8 View commit details
    Browse the repository at this point in the history

  3. Update article_is_retracted

    @kkaris
    kkaris committed Dec 18, 2023
    Configuration menu
    Copy the full SHA
    9b42082 View commit details
    Browse the repository at this point in the history

Commits on Dec 19, 2023

  1. Fix bug

    @kkaris
    kkaris committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    006ae93 View commit details
    Browse the repository at this point in the history

Commits on Dec 31, 2023

  1. Clean up retraction implementation

    @bgyori
    bgyori committed Dec 31, 2023
    Configuration menu
    Copy the full SHA
    b5f3a0e View commit details
    Browse the repository at this point in the history

  2. Change the retractions API and resource name

    @bgyori
    bgyori committed Dec 31, 2023
    Configuration menu
    Copy the full SHA
    8bed86e View commit details
    Browse the repository at this point in the history