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remote_files: Add support for directly using local cache - #87
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joverlee521 wants to merge 2 commits into
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joverlee521 wants to merge 2 commits into
joverlee521 wants to merge 2 commits into
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The Snakemake storage usually checks the existence and revalidates remote files before using the local cache, which can lead to errors when running the workflow offline even if the local cache already exists. This change adds support to directly use the local cache if it exists and bypass the remote file check when 1. the config parameter `use_remote_files` is False 2. the environment variable `NEXTSTRAIN_REMOTE_FILES` is False 3. the workflow is running offline Based on discussions in <nextstrain/public#47> and changes tested in measles repo <nextstrain/measles@60634e2...b238682>
This was referenced Oct 1, 2026
jameshadfield
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Thanks for taking this on and turning the prototype into a polished PR! I haven't tested the code but reading through it I think the behaviour is spot on. One minor query re: env variables is the only thing that stuck out to me.
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| def is_online(host="8.8.8.8", port=53, timeout=3) -> bool: | ||
| """ | ||
| Check if workflow has network connection. | ||
| Based on <https://stackoverflow.com/a/33117579> | ||
| Host: 8.8.8.8 (google-public-dns-a.google.com) | ||
| OpenPort: 53/tcp | ||
| Service: domain (DNS/TCP) | ||
| """ |
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Cool! I like this general "is online" approach better than the per-source checks in my original prototype
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On the other hand, by checking against Google, is_online could return True when sources are unavailable, or False when sources are available but Google is down. This is very edge case-y though, I think it's fine to keep as-is.
Based on discussion in review <#87 (comment)>
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Will merge this next Tuesday to monitor downstream uses. |
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Description of proposed changes
The Snakemake storage usually checks the existence and revalidates remote files before using the local cache, which can lead to errors when running the workflow offline even if the local cache already exists.
This change adds support to directly use the local cache if it exists and bypass the remote file check when
use_remote_filesis FalseNEXTSTRAIN_REMOTE_FILESis FalseBased on discussions in nextstrain/public#47 and changes tested in measles repo
nextstrain/measles@60634e2...b238682
Related issue(s)
Part of nextstrain/public#47
Checklist
If adding a script, add an entry for it in the README.