Truenat Ultra — Rapid TB Diagnostics Pipeline
BCHPR · TB Reference Laboratory Bamenda · 2023 – present
1,828-line pipeline for Truenat Ultra rapid TB PCR instruments — incremental ingestion with MD5-based change detection, SQLite state tracking, and Polars-optimised consolidation across a distributed lab network.
Highlights
- FileTracker class — SQLite-backed MD5 hashing skips re-processing of unchanged files.
- ThreadPoolExecutor parallel processing across files with per-file success / failure status.
- Polars DataFrames for speed on large export sets.
- File locking to prevent race conditions in multi-user environments.
- Comprehensive logging (truenat_processing.log) with row counts, file sizes, and modification times per import.
- Bilingual record harmonisation and automatic encoding standardisation.
- Supports pooled-testing cost-effectiveness research alongside GeneXpert data.
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