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Fix ranks like "domain" being rewritten to "no rank" on save #83

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Merged
audy merged 2 commits into from
Nov 5, 2026
Merged

Fix ranks like "domain" being rewritten to "no rank" on save #83

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d38ca5d
Fix ranks like "domain" being rewritten to "no rank" on save
audy Nov 4, 2026
800c833
Consolidate T bound in ncbi::save to satisfy clippy multiple_bound_lo…
audy Nov 4, 2026
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12 changes: 6 additions & 6 deletions src/formats/ncbi.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -83,12 +83,9 @@
Ok(gt)
}

pub fn save<'t, T: 't, P: AsRef<Path>, X: Taxonomy<'t, T>>(
tax: &'t X,
out_dir: P,
) -> TaxonomyResult<()>
pub fn save<'t, T, P: AsRef<Path>, X: Taxonomy<'t, T>>(tax: &'t X, out_dir: P) -> TaxonomyResult<()>
where
T: Clone + Debug + Display + PartialEq,
T: 't + Clone + Debug + Display + PartialEq,
{
let dir = out_dir.as_ref();
std::fs::create_dir_all(dir)?;
Expand All @@ -107,7 +104,7 @@
.unwrap_or_default()
};
name_writer
.write_all(format!("{}\t|\t{}\t|\t\t|\tscientific name\t|\n", &key, name).as_bytes())?;

Check warning on line 107 in src/formats/ncbi.rs

View workflow job for this annotation

GitHub Actions / clippy 

redundant reference in `format!` argument
node_writer.write_all(
format!(
"{}\t|\t{}\t|\t{}\t|\t\t|\t\t|\t\t|\t\t|\t\t|\t\t|\t\t|\t\t|\t\t|\t\t|\n",
Expand All @@ -134,7 +131,7 @@
let nodes =
"1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
10239\t|\t1\t|\tno_rank\t|\t\t|\t9\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
2\t|\t131567\t|\tdomain\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|
543\t|\t91347\t|\tfamily\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|
561\t|\t543\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|
562\t|\t561\t|\tspecies\t|\tEC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|
Expand Down Expand Up @@ -239,6 +236,9 @@
Some(("561", 1.))
);

// Check Bacteria (2) keeps its "domain" rank through save/load
assert_eq!(Taxonomy::<&str>::rank(&tax2, "2").unwrap(), TaxRank::Domain);

// Check Escherichia (561)
assert_eq!(Taxonomy::<&str>::name(&tax2, "561").unwrap(), "Escherichia");
assert_eq!(
Expand Down
194 changes: 78 additions & 116 deletions src/rank.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -111,61 +111,115 @@ pub enum TaxRank {
}

impl TaxRank {
/// Converts a TaxRank into a one of the rank strings NCBI uses.
/// Note that this doesn't handle ranks that are not used by the NCBI taxonomy.
/// Converts a TaxRank into the rank string NCBI uses (or, for ranks NCBI
/// doesn't define, our own lowercase spelling). Never coerces to "no rank".
pub fn to_ncbi_rank(self) -> &'static str {
self.as_str()
}

pub fn as_str(self) -> &'static str {
match self {
TaxRank::Superkingdom => "superkingdom",
TaxRank::Domain => "domain",
TaxRank::AcellularRoot => "acellular root",
TaxRank::CellularRoot => "cellular root",
TaxRank::Subdomain => "subdomain",
TaxRank::Realm => "realm",
TaxRank::Subrealm => "subrealm",
TaxRank::Hyperkingdom => "hyperkingdom",
TaxRank::Superkingdom => "superkingdom",
TaxRank::Kingdom => "kingdom",
TaxRank::Subkingdom => "subkingdom",
TaxRank::Infrakingdom => "infrakingdom",
TaxRank::Parvkingdom => "parvkingdom",
TaxRank::Superphylum => "superphylum",
TaxRank::Phylum => "phylum",
TaxRank::Subphylum => "subphylum",
TaxRank::Infraphylum => "infraphylum",
TaxRank::Microphylum => "microphylum",
TaxRank::Superclass => "superclass",
TaxRank::Class => "class",
TaxRank::Subclass => "subclass",
TaxRank::Infraclass => "infraclass",
TaxRank::Parvclass => "parvclass",
TaxRank::Superdivision => "superdivision",
TaxRank::Division => "division",
TaxRank::Subdivision => "subdivision",
TaxRank::Infradivision => "infradivision",
TaxRank::Superlegion => "superlegion",
TaxRank::Legion => "legion",
TaxRank::Sublegion => "sublegion",
TaxRank::Infralegion => "infralegion",
TaxRank::Supercohort => "supercohort",
TaxRank::Cohort => "cohort",
TaxRank::Subcohort => "subcohort",
TaxRank::Infracohort => "infracohort",
TaxRank::Superorder => "superorder",
TaxRank::Gigaorder => "gigaorder",
TaxRank::Magnorder => "magnorder",
TaxRank::Grandorder => "grandorder",
TaxRank::Mirorder => "mirorder",
TaxRank::SeriesFish => "series fish",
TaxRank::Order => "order",
TaxRank::Nanorder => "nanorder",
TaxRank::Hypoorder => "hypoorder",
TaxRank::Minorder => "minorder",
TaxRank::Suborder => "suborder",
TaxRank::Infraorder => "infraorder",
TaxRank::Parvorder => "parvorder",
TaxRank::Section => "section",
TaxRank::Subsection => "subsection",
TaxRank::Gigafamily => "gigafamily",
TaxRank::Megafamily => "megafamily",
TaxRank::Grandfamily => "grandfamily",
TaxRank::Hyperfamily => "hyperfamily",
TaxRank::Superfamily => "superfamily",
TaxRank::Epifamily => "epifamily",
TaxRank::SeriesLepidoptera => "series lepidoptera",
TaxRank::GroupLepidoptera => "group lepidoptera",
TaxRank::Family => "family",
TaxRank::Subfamily => "subfamily",
TaxRank::Infrafamily => "infrafamily",
TaxRank::Supertribe => "supertribe",
TaxRank::Tribe => "tribe",
TaxRank::Subtribe => "subtribe",
TaxRank::Infratribe => "infratribe",
TaxRank::Genus => "genus",
TaxRank::Series => "series",
TaxRank::Subgenus => "subgenus",
TaxRank::Series => "series",
TaxRank::SubseriesBotany => "subseries botany",
TaxRank::SpeciesGroup => "species group",
TaxRank::SpeciesSubgroup => "species subgroup",
TaxRank::Species => "species",
TaxRank::Subspecies => "subspecies",
TaxRank::Strain => "strain",
TaxRank::Synthetic => "synthetic",
TaxRank::Varietas => "varietas",
TaxRank::Subvarietas => "subvarietas",
TaxRank::Forma => "forma",
TaxRank::Unspecified => "no rank",
TaxRank::Clade => "clade",
TaxRank::Subforma => "subforma",
TaxRank::Cultivar => "cultivar",
TaxRank::Breed => "breed",
TaxRank::Strain => "strain",
TaxRank::Individual => "individual",
TaxRank::SeroGroup => "serogroup",
TaxRank::Unspecified => "no rank",
TaxRank::Biotype => "biotype",
TaxRank::Clade => "clade",
TaxRank::FormaSpecialis => "forma specialis",
TaxRank::Isolate => "isolate",
TaxRank::Serotype => "serotype",
TaxRank::Genotype => "genotype",
TaxRank::Morph => "morph",
TaxRank::Pathogroup => "pathogroup",
// TODO: not sure if we want to manually coerce everything like this?
_ => "no rank",
TaxRank::Synthetic => "synthetic",
}
}
}

impl fmt::Display for TaxRank {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(f, "{}", self.as_str())
}
}

impl FromStr for TaxRank {
type Err = Error;

Expand Down Expand Up @@ -195,8 +249,10 @@ impl FromStr for TaxRank {
"subclass" | "subclassis" => Ok(TaxRank::Subclass),
"infraclass" => Ok(TaxRank::Infraclass),
"parvclass" => Ok(TaxRank::Parvclass),
// note "division" may be either a TaxRank::Division (zoological)
// or synonym for TaxRank::Phylum (botanical) so we don't impl here
"superdivision" => Ok(TaxRank::Superdivision),
"division" => Ok(TaxRank::Division),
"subdivision" => Ok(TaxRank::Subdivision),
"infradivision" => Ok(TaxRank::Infradivision),
"superlegion" => Ok(TaxRank::Superlegion),
"legion" => Ok(TaxRank::Legion),
"sublegion" => Ok(TaxRank::Sublegion),
Expand All @@ -210,6 +266,7 @@ impl FromStr for TaxRank {
"magnorder" => Ok(TaxRank::Magnorder),
"grandorder" => Ok(TaxRank::Grandorder),
"mirorder" => Ok(TaxRank::Mirorder),
"series fish" => Ok(TaxRank::SeriesFish),
"order" | "ordo" => Ok(TaxRank::Order),
"nanorder" => Ok(TaxRank::Nanorder),
"hypoorder" => Ok(TaxRank::Hypoorder),
Expand All @@ -225,6 +282,8 @@ impl FromStr for TaxRank {
"hyperfamily" => Ok(TaxRank::Hyperfamily),
"superfamily" => Ok(TaxRank::Superfamily),
"epifamily" => Ok(TaxRank::Epifamily),
"series lepidoptera" => Ok(TaxRank::SeriesLepidoptera),
"group lepidoptera" => Ok(TaxRank::GroupLepidoptera),
"family" | "familia" => Ok(TaxRank::Family),
"subfamily" => Ok(TaxRank::Subfamily),
"infrafamily" => Ok(TaxRank::Infrafamily),
Expand All @@ -235,6 +294,7 @@ impl FromStr for TaxRank {
"genus" | "genera" => Ok(TaxRank::Genus),
"subgenus" => Ok(TaxRank::Subgenus),
"series" => Ok(TaxRank::Series),
"subseries botany" => Ok(TaxRank::SubseriesBotany),
"species group" => Ok(TaxRank::SpeciesGroup),
"species subgroup" => Ok(TaxRank::SpeciesSubgroup),
"species" => Ok(TaxRank::Species),
Expand All @@ -247,6 +307,7 @@ impl FromStr for TaxRank {
"cultivar" => Ok(TaxRank::Cultivar),
"breed" => Ok(TaxRank::Breed),
"strain" => Ok(TaxRank::Strain),
"individual" => Ok(TaxRank::Individual),
"serogroup" => Ok(TaxRank::SeroGroup),
"no rank" | "no_rank" => Ok(TaxRank::Unspecified),
"biotype" => Ok(TaxRank::Biotype),
Expand All @@ -262,105 +323,6 @@ impl FromStr for TaxRank {
}
}

impl fmt::Display for TaxRank {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
let rank_str = match self {
TaxRank::Domain => "domain",
TaxRank::AcellularRoot => "acellular root",
TaxRank::CellularRoot => "cellular root",
TaxRank::Subdomain => "subdomain",
TaxRank::Realm => "realm",
TaxRank::Subrealm => "subrealm",
TaxRank::Hyperkingdom => "hyperkingdom",
TaxRank::Superkingdom => "superkingdom",
TaxRank::Kingdom => "kingdom",
TaxRank::Subkingdom => "subkingdom",
TaxRank::Infrakingdom => "infrakingdom",
TaxRank::Parvkingdom => "parvkingdom",
TaxRank::Superphylum => "superphylum",
TaxRank::Phylum => "phylum",
TaxRank::Subphylum => "subphylum",
TaxRank::Infraphylum => "infraphylum",
TaxRank::Microphylum => "microphylum",
TaxRank::Superclass => "superclass",
TaxRank::Class => "class",
TaxRank::Subclass => "subclass",
TaxRank::Infraclass => "infraclass",
TaxRank::Parvclass => "parvclass",
TaxRank::Superdivision => "superdivision",
TaxRank::Division => "division",
TaxRank::Subdivision => "subdivision",
TaxRank::Infradivision => "infradivision",
TaxRank::Superlegion => "superlegion",
TaxRank::Legion => "legion",
TaxRank::Sublegion => "sublegion",
TaxRank::Infralegion => "infralegion",
TaxRank::Supercohort => "supercohort",
TaxRank::Cohort => "cohort",
TaxRank::Subcohort => "subcohort",
TaxRank::Infracohort => "infracohort",
TaxRank::Superorder => "superorder",
TaxRank::Gigaorder => "gigaorder",
TaxRank::Magnorder => "magnorder",
TaxRank::Grandorder => "grandorder",
TaxRank::Mirorder => "mirorder",
TaxRank::SeriesFish => "series fish",
TaxRank::Order => "order",
TaxRank::Nanorder => "nanorder",
TaxRank::Hypoorder => "hypoorder",
TaxRank::Minorder => "minorder",
TaxRank::Suborder => "suborder",
TaxRank::Infraorder => "infraorder",
TaxRank::Parvorder => "parvorder",
TaxRank::Section => "section",
TaxRank::Subsection => "subsection",
TaxRank::Gigafamily => "gigafamily",
TaxRank::Megafamily => "megafamily",
TaxRank::Grandfamily => "grandfamily",
TaxRank::Hyperfamily => "hyperfamily",
TaxRank::Superfamily => "superfamily",
TaxRank::Epifamily => "epifamily",
TaxRank::SeriesLepidoptera => "series lepidoptera",
TaxRank::GroupLepidoptera => "group lepidoptera",
TaxRank::Family => "family",
TaxRank::Subfamily => "subfamily",
TaxRank::Infrafamily => "infrafamily",
TaxRank::Supertribe => "supertribe",
TaxRank::Tribe => "tribe",
TaxRank::Subtribe => "subtribe",
TaxRank::Infratribe => "infratribe",
TaxRank::Genus => "genus",
TaxRank::Subgenus => "subgenus",
TaxRank::Series => "series",
TaxRank::SubseriesBotany => "subseries botany",
TaxRank::SpeciesGroup => "species group",
TaxRank::SpeciesSubgroup => "species subgroup",
TaxRank::Species => "species",
TaxRank::Subspecies => "subspecies",
TaxRank::Varietas => "varietas",
TaxRank::Subvarietas => "subvarietas",
TaxRank::Forma => "forma",
TaxRank::Subforma => "subforma",
TaxRank::Cultivar => "cultivar",
TaxRank::Breed => "breed",
TaxRank::Strain => "strain",
TaxRank::Individual => "individual",
TaxRank::SeroGroup => "serogroup",
TaxRank::Unspecified => "no rank",
TaxRank::Biotype => "biotype",
TaxRank::Clade => "clade",
TaxRank::FormaSpecialis => "forma specialis",
TaxRank::Isolate => "isolate",
TaxRank::Serotype => "serotype",
TaxRank::Genotype => "genotype",
TaxRank::Morph => "morph",
TaxRank::Pathogroup => "pathogroup",
TaxRank::Synthetic => "synthetic",
};
write!(f, "{}", rank_str)
}
}

#[cfg(test)]
mod test {
use super::TaxRank;
Expand Down Expand Up @@ -461,7 +423,7 @@ mod test {
#[test]
fn test_str_to_rank() {
for rank in RANKS.iter() {
assert!(TaxRank::from_str(rank.to_ncbi_rank()).is_ok());
assert_eq!(TaxRank::from_str(rank.to_ncbi_rank()).unwrap(), *rank);
}
assert!(TaxRank::from_str("fake_data").is_err());
}
Expand All @@ -471,11 +433,11 @@ mod test {
for rank in RANKS.iter() {
let rank_str = rank.to_string();
assert!(!rank_str.is_empty());

let ncbi_str = rank.to_ncbi_rank();
if ncbi_str != "no rank" {
assert_eq!(ncbi_str, rank_str);
assert_eq!(rank.to_ncbi_rank(), rank_str);
if *rank != Unspecified {
assert_ne!(rank_str, "no rank");
}
}
assert_eq!(Domain.to_ncbi_rank(), "domain");
}
}
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