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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
1.5 KiB
1.5 KiB
obidefault Package: Configuration State Management
This Go package provides a centralized, thread-safe(ish) configuration layer for taxonomy-related settings in the OBIDMS (Open Biological and Biomedical Data Management System) framework. It exposes simple getters, setters, and pointer accessors for four core boolean/string flags that control how taxonomic identifiers (taxids) are handled during data processing.
Core Configuration Flags
__taxonomy__: Stores the currently selected taxonomy (e.g.,"NCBI","UNIPROT").__alternative_name__: Enables/disables use of alternative taxonomic names (e.g., synonyms).__fail_on_taxonomy__: If true, processing halts on taxonomy mismatches/errors.__update_taxid__: If true, taxids are auto-updated to current NCBI/DB versions.__raw_taxid__: If true, raw (unprocessed) taxids are preserved instead of normalized.
Public API
- Getters:
UseRawTaxids(),SelectedTaxonomy(),HasSelectedTaxonomy(), etc., return current values. - Pointer Accessors: e.g.,
SelectedTaxonomyPtr()returns a pointer for direct mutation (advanced use). - Setters:
SetSelectedTaxonomy(),SetAlternativeNamesSelected(), etc., update state.
Use Case
Typically used at application startup to configure global behavior (e.g., SetSelectedTaxonomy("NCBI"), SetUpdateTaxid(true)), then referenced by downstream modules during data import, validation, or mapping. Minimalist and explicit—no external dependencies.