snakemake / snakemake/snakemake
add connection pooling for remote objects
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- Dominant language
- Python
- Stars
- 2.9k
- Forks
- 656
- Avg merge
- 4d 12h
- Merged PRs (30d)
- 9
Description
Is your feature request related to a problem? Please describe.
I have a workflow for downloading the latest version of RefSeq. However, there are a few thousand protein files to download. Using FTP remote to download the files is untenable. I gave up after waiting a day for the DAG to resolve.
Describe the solution you'd like
I hacked remote/FTP.py to use connection pooling (https://github.com/niciqy/ConnectionPool) and it was able to resolve the DAG in under half an hour.
For a different workflow with only a dozen files, it cut the dry-run time from 30s to 20s.
I've only looked at the FTP module so far, and I only partially understand how the whole Remote system is built, but it could be a way to speed up any workflow using remote resources.
Describe alternatives you've considered
I can make my workflow functional by manually checking the dates and downloading with wget or curl, but that requires more code in the workflow than simply using remotes.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with remote/FTP.py and trace how the broader Remote system creates and reuses connections. Compare the existing FTP behavior with the reported connection-pooling approach, then verify that workflows using many remote resources resolve substantially faster without breaking smaller remote workflows.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- networking
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100