Add TSV-backed machine type loader with in-memory cache and fallback warnings#20
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Add TSV-backed machine type loader with in-memory cache and fallback warnings#20
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Pull request overview
This pull request replaces the hardcoded MACHINE_TYPES dictionary with a dynamic loader that fetches machine type mappings from a remote TSV file, with fallback to a bundled mapping when the remote resource is unavailable.
Changes:
- Introduces
load_machine_types()function that fetches and caches machine type mappings from a remote TSV URL with fallback to bundled mappings - Renames
MACHINE_TYPEStoMACHINE_TYPES_FALLBACKand adds remote URL configuration - Updates three call sites to use the new
load_machine_types()function instead of direct dictionary access
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Motivation
machine_types.tsvto resolve Illumina instrument codes instead of a hardcoded map.Description
MACHINE_TYPES_FALLBACK(bundled fallback),MACHINE_TYPES_URL, and an in-memory cache_machine_types_cachewith a newload_machine_types()loader that fetches and parses the TSV viaurlopenandcsvand warns on fallback.load_machine_types()inIlluminaDir._parse_folder,IlluminaFastq.machine_type, and the run-name detection logic.warnings.warnmessages when the remote TSV cannot be loaded or contains no valid rows, and document the fallback mapping inline with a comment.csv,warnings,URLError,urlopen) and keep caching only in-memory (no disk writes).Testing
Codex Task