Public helper APIs¶

These helpers are supported at the module or class paths below. Use parse for complete parsing policy. Lower-level helpers have deliberately narrower contracts; they do not establish that an allele or species is biologically valid. Direct tests and internal callers use the same public names.

Inputs and table rows¶

• mhcgnomes.input_validation.validate_mhc_input(value, raise_on_error=True) returns True for strings. Scalar missing inputs return False in tolerant mode or raise ParseError; other types raise TypeError. It does not coerce strings or tokenize them.
• mhcgnomes.parse_outcome_to_row(raw_input, outcome) accepts a Result, ParseError, or None. It returns a new dictionary with input, type, normalized, compact, species, gene_name, mhc_class, properties, and error, plus available to_record() fields. gene_name is short; legacy gene fields retain their full identifier. The input is preserved. A successful Haplotype still has a row without a record schema. Unsupported outcome types raise TypeError; serialization errors propagate except for NotImplementedError from the optional record schema.
• mhcgnomes.cli.outcome_to_cli_row(raw_input, outcome) projects that row into the CLI's existing eight string columns, using gene_name for its gene display. It has the same outcome/error contract.

Parser building blocks¶

Public API	Inputs and result	Scope
mhcgnomes.parser.blank_locus_gene_name(member)	String to gene-name string or None	Recognizes exactly one star and a case-insensitive Blank/null field; trims whitespace. Does not look up the gene.
Parser.find_matching_name_and_parse_alleles(query_name, name_to_alleles_dict, species)	Query string, NormalizingDictionary of member-name sequences, and Species; returns (canonical_name, members, absent_genes) or None	Curated haplotype/serotype definitions. Invalid members emit UserWarning and are omitted. Other errors propagate.
Parser.parse_explicit_species_allele_candidates(name)	String to list of transformed Allele candidates	Narrow path for explicit species and at least two numeric fields. Returns [] outside that grammar, for non-strings, or in verbose mode; caller chooses whether to fall back. Applies this Parser's alias/transform settings.
Parser.parse_renamed_allele(species, source_gene, source_mhc_class, target_gene_name, target_allele_name, raw_string)	Species, optional source Gene/class, optional target gene name, target allele string, optional raw input; returns Allele, AlleleWithoutGene, or None	Constructs a rename target, preserving source class for geneless targets. Unknown genes or unparseable targets return None. This does not apply or transfer mutations. See the full parameter docstring.

Species naming and curation¶

The following functions live in mhcgnomes.species. Scientific names and prefixes are strings unless noted. They perform no network lookup and do not turn a mechanically derived prefix into evidence of published usage.

Function	Result and scope
make_long_prefix(latin_name)	Generated 4+4 string from the first two valid scientific-name words, or None. This is the library's compatibility shorthand, not the official 2+2 nomenclature rule; it does not check collisions.
binomial_long_prefix(latin_name)	Same shorthand only for a binomial; returns None for a trinomial, group, or unsuitable name. It does not check uniqueness.
generated_long_prefix_count(prefix)	Number of modeled binomials claiming the exact case-sensitive 4+4 string; zero if unknown. Does not mutate the ontology.
auto_generated_prefixes_for_latin_name(latin_name)	New ordered list: concatenated binomial first, then a 4+4 shorthand only if unique in the bundled ontology. Non-binomials return an empty list. Unknown binomials can still produce a full-name string.
derive_prefix_provenance(prefix, latin_name)	"generated", "group label", or None, using only derivation and bundled ontology. Never asserts "designated"; that requires source evidence.
containing_species(species_objects)	Unique claimant containing all others by ancestry, or None. Accepts a collection of distinct Species; empty or unrelated collections return None.
hyphens_as_spaces(identifier)	New string with hyphens replaced by spaces only when the string already has both; otherwise None, including non-string input. Used for lookup spelling variants.
blocked_registry_prefixes()	New set of normalized prefix keys whose bundled curation status is blocked or registry_only. Takes no arguments and does not change that registry.

mhcgnomes.allele.single_field_allele_names() returns a cached read-only mapping from (scientific species name, canonical gene name) to a frozenset of historical complete one-field name strings. It supports the naming classifier; it is not a current registry-membership API. Unknown species/genes in the source table are omitted.

Verified download transport¶

mhcgnomes.external_data.download_to_cache(url, source, cache_path, retries=3) is the low-level verified transport. source is a Source carrying the expected SHA-256; cache_path is a pathlib.Path. The function creates parent directories, downloads to a temporary file, checks its digest, then atomically replaces the destination. It returns None. It retries transient HTTP/network failures up to the total attempt count and removes temporary files on failure. Checksum failures and terminal transfer failures raise ExternalDataError; other local filesystem errors can propagate as OSError. Use resolve_source for normal cache, mirror, and offline resolution.

The separate source-generation API and its precedence rules are documented in External data.