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.

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

Replace sequential PubMed load with a parallel process #379

Open
gaurav opened this issue Dec 12, 2024 · 0 comments
Open

Replace sequential PubMed load with a parallel process #379

gaurav opened this issue Dec 12, 2024 · 0 comments

Comments

@gaurav
Copy link
Collaborator

gaurav commented Dec 12, 2024

I originally went with a sequential PubMed load because that would load publications in the order of update, allowing e.g. a later retitled publication to overwrite a previously titled one. However, loading all the 1,628 PubMed files sequentially takes a long time!

Some better ideas:

  1. Convert all files into individual DuckDB databases, then run one query over all of them to ascertain the most recent title/publication status for each one.
  2. Convert all files into e.g. TSV files in parallel, then run through the smaller TSV file sequentially to figure out most recent title/publication status.
  3. ???
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant