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https://github.com/metabarcoding/obitools4.git
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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)
22 lines
1.5 KiB
Markdown
22 lines
1.5 KiB
Markdown
# `obidefault` Package: Configuration State Management
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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.
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## Core Configuration Flags
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- `__taxonomy__`: Stores the currently selected taxonomy (e.g., `"NCBI"`, `"UNIPROT"`).
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- `__alternative_name__`: Enables/disables use of alternative taxonomic names (e.g., synonyms).
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- `__fail_on_taxonomy__`: If true, processing halts on taxonomy mismatches/errors.
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- `__update_taxid__`: If true, taxids are auto-updated to current NCBI/DB versions.
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- `__raw_taxid__`: If true, raw (unprocessed) taxids are preserved instead of normalized.
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## Public API
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- **Getters**: `UseRawTaxids()`, `SelectedTaxonomy()`, `HasSelectedTaxonomy()`, etc., return current values.
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- **Pointer Accessors**: e.g., `SelectedTaxonomyPtr()` returns a pointer for direct mutation (advanced use).
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- **Setters**: `SetSelectedTaxonomy()`, `SetAlternativeNamesSelected()`, etc., update state.
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## Use Case
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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.
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