Merge pull request #67 from unipept/fix/ncbi-rank-updates

pverscha · web-flow · commit 4c66f08f0905 · 2025-03-20T14:17:09.000+01:00
Prepare the Unipept API for the newest NCBI taxonomy
diff --git a/api/src/controllers/api/pept2lca.rs b/api/src/controllers/api/pept2lca.rs
@@ -87,7 +87,7 @@ async fn handler(
 }
 
 generate_handlers! (
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/controllers/api/pept2taxa.rs b/api/src/controllers/api/pept2taxa.rs
@@ -120,7 +120,7 @@ async fn handler(
 }
 
 generate_handlers! (
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/controllers/api/peptinfo.rs b/api/src/controllers/api/peptinfo.rs
@@ -110,7 +110,7 @@ async fn handler(
 }
 
 generate_handlers! (
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/controllers/api/protinfo.rs b/api/src/controllers/api/protinfo.rs
@@ -105,7 +105,7 @@ async fn handler(
 }
 
 generate_handlers! (
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/controllers/api/taxa2lca.rs b/api/src/controllers/api/taxa2lca.rs
@@ -80,7 +80,7 @@ async fn handler(
 }
 
 generate_handlers! (
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/controllers/api/taxa2tree.rs b/api/src/controllers/api/taxa2tree.rs
@@ -83,7 +83,7 @@ fn handler(
 }
 
 generate_handlers!(
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         GetContent(params) => GetContent<GetParameters>,
@@ -94,7 +94,7 @@ generate_handlers!(
 );
 
 generate_handlers!(
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         PostContent(params) => PostContent<PostParameters>,
@@ -105,7 +105,7 @@ generate_handlers!(
 );
 
 generate_handlers!(
-    [ V1, V2 ]
+    [ V2 ]
     async fn html_handler(
         state => State<AppState>,
         GetContent(params) => GetContent<GetParameters>,
@@ -123,7 +123,7 @@ generate_handlers!(
 );
 
 generate_handlers!(
-    [ V1, V2 ]
+    [ V2 ]
     async fn html_handler(
         state => State<AppState>,
         PostContent(params) => PostContent<PostParameters>,
diff --git a/api/src/controllers/api/taxonomy.rs b/api/src/controllers/api/taxonomy.rs
@@ -119,13 +119,13 @@ async fn handler(
                 // If descendants is true, we need to get all the taxa at the requested level and
                 // report those as children of the root.
                 if descendants {
-                    children = Some(lineage_store.get_all_taxon_ids_at_rank("superkingdom")?
+                    children = Some(lineage_store.get_all_taxon_ids_at_rank("domain")?
                         .iter()
                         .flat_map(|sk_taxon| {
                             descendants_ranks
                                 .iter()
                                 .cloned()
-                                .filter_map(|desc_rank| get_children_at_rank(*sk_taxon, LineageRank::Superkingdom, desc_rank, lineage_store))
+                                .filter_map(|desc_rank| get_children_at_rank(*sk_taxon, LineageRank::Domain, desc_rank, lineage_store))
                                 .flat_map(|set| set.into_iter())
                                 .collect::<Vec<u32>>()
                         })
@@ -197,7 +197,7 @@ async fn handler(
 }
 
 generate_handlers!(
-    [ V1, V2 ]
+    [ V2 ]
     async fn json_handler(
         state => State<AppState>,
         params => Parameters,
diff --git a/api/src/helpers/lca_helper.rs b/api/src/helpers/lca_helper.rs
@@ -11,12 +11,12 @@ pub fn calculate_lca(
     lineage_store: &LineageStore
 ) -> i32 {
     let cleaned_taxa = taxa.into_iter().filter(|&taxon_id| taxon_store.is_valid(taxon_id));
-
+    
     let lineages: Vec<Vec<i32>> = cleaned_taxa
         .into_iter()
         .map(|taxon_id| get_lineage_array_numeric(taxon_id, version, lineage_store))
         .collect();
-
+    
     let amount_of_ranks = get_amount_of_ranks(version);
     let genus_index = get_genus_index(version);
     let species_index = get_species_index(version);
diff --git a/api/src/helpers/lineage_helper/mod.rs b/api/src/helpers/lineage_helper/mod.rs
@@ -1,4 +1,3 @@
-pub mod v1;
 pub mod v2;
 
 use datastore::{LineageStore, TaxonStore};
@@ -60,7 +59,7 @@ macro_rules! create_lineages {
 
             pub fn get_lineage_array_numeric(taxon_id: u32, lineage_store: &LineageStore) -> Vec<i32> {
                 let lineage = lineage_store.get(taxon_id).cloned().unwrap_or_default();
-
+                
                 vec![
                     $(
                         get_id(lineage.$field).unwrap_or(0),
@@ -70,7 +69,7 @@ macro_rules! create_lineages {
 
             pub fn get_lineage_with_names(taxon_id: u32, lineage_store: &LineageStore, taxon_store: &TaxonStore) -> Option<LineageWithNames> {
                 let lineage = lineage_store.get(taxon_id)?;
-
+                
                 Some(LineageWithNames {
                     $(
                         [<$field _id>]: get_id(lineage.$field),
@@ -96,83 +95,70 @@ pub(crate) use create_lineages;
 
 #[derive(Clone, Copy)]
 pub enum LineageVersion {
-    V1,
     V2
 }
 
 #[derive(Serialize, Debug)]
 #[serde(untagged)]
+#[allow(clippy::large_enum_variant)]
 pub enum Lineage {
-    DefaultV1(v1::Lineage),
-    NamesV1(v1::LineageWithNames),
     DefaultV2(v2::Lineage),
     NamesV2(v2::LineageWithNames)
 }
 
 pub fn get_lineage(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Option<Lineage> {
     match version {
-        LineageVersion::V1 => v1::get_lineage(taxon_id, lineage_store).map(Lineage::DefaultV1),
         LineageVersion::V2 => v2::get_lineage(taxon_id, lineage_store).map(Lineage::DefaultV2)
     }
 }
 
 pub fn get_empty_lineage(version: LineageVersion) -> Option<Lineage> {
     match version {
-        LineageVersion::V1 => v1::get_empty_lineage().map(Lineage::DefaultV1),
         LineageVersion::V2 => v2::get_empty_lineage().map(Lineage::DefaultV2)
     }
 }
 
 pub fn get_lineage_array(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Vec<Option<i32>> {
     match version {
-        LineageVersion::V1 => v1::get_lineage_array(taxon_id, lineage_store),
         LineageVersion::V2 => v2::get_lineage_array(taxon_id, lineage_store)
     }
 }
 
 pub fn get_lineage_array_numeric(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Vec<i32> {
     match version {
-        LineageVersion::V1 => v1::get_lineage_array_numeric(taxon_id, lineage_store),
         LineageVersion::V2 => v2::get_lineage_array_numeric(taxon_id, lineage_store)
     }
 }
 
 pub fn get_lineage_with_names(
     taxon_id: u32,
-    version: LineageVersion,
+    _version: LineageVersion,
     lineage_store: &LineageStore,
     taxon_store: &TaxonStore
 ) -> Option<Lineage> {
-    match version {
-        LineageVersion::V1 => v1::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV1),
-        LineageVersion::V2 => v2::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV2)
-    }
+    v2::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV2)
 }
 
 pub fn get_empty_lineage_with_names(version: LineageVersion) -> Option<Lineage> {
     match version {
-        LineageVersion::V1 => v1::get_empty_lineage_with_names().map(Lineage::NamesV1),
         LineageVersion::V2 => v2::get_empty_lineage_with_names().map(Lineage::NamesV2)
     }
 }
 
 pub fn get_amount_of_ranks(version: LineageVersion) -> u8 {
     match version {
-        LineageVersion::V1 => 28,
-        LineageVersion::V2 => 27
+        LineageVersion::V2 => 28
     }
 }
 
 pub fn get_genus_index(version: LineageVersion) -> u8 {
     match version {
-        LineageVersion::V1 => 20,
-        LineageVersion::V2 => 18
+        LineageVersion::V2 => 19
     }
 }
 
 pub fn get_species_index(version: LineageVersion) -> u8 {
     match version {
-        LineageVersion::V1 => 24,
-        LineageVersion::V2 => 22
+        LineageVersion::V2 => 23
     }
 }
diff --git a/api/src/helpers/lineage_helper/v1.rs b/api/src/helpers/lineage_helper/v1.rs
diff --git a/api/src/helpers/lineage_helper/v2.rs b/api/src/helpers/lineage_helper/v2.rs
@@ -5,7 +5,8 @@ use serde::Serialize;
 use super::create_lineages;
 
 create_lineages!(
-    superkingdom,
+    domain,
+    realm,
     kingdom,
     subkingdom,
     superphylum,
diff --git a/api/src/routes.rs b/api/src/routes.rs
@@ -44,7 +44,7 @@ pub fn create_router(state: AppState) -> Router {
 }
 
 fn create_api_routes() -> Router<AppState> {
-    Router::new().nest("/v1", create_api_v1_routes()).nest("/v2", create_api_v2_routes())
+    Router::new().nest("/v1", create_api_v2_routes()).nest("/v2", create_api_v2_routes())
 }
 
 macro_rules! define_routes {
@@ -65,36 +65,6 @@ macro_rules! define_routes {
 
 pub(crate) use define_routes;
 
-fn create_api_v1_routes() -> Router<AppState> {
-    define_routes!(
-        "/pept2ec",
-        get(pept2ec::get_json_handler).post(pept2ec::post_json_handler),
-        "/pept2funct",
-        get(pept2funct::get_json_handler).post(pept2funct::post_json_handler),
-        "/pept2go",
-        get(pept2go::get_json_handler).post(pept2go::post_json_handler),
-        "/pept2interpro",
-        get(pept2interpro::get_json_handler).post(pept2interpro::post_json_handler),
-        "/pept2lca",
-        get(pept2lca::get_json_handler_v1).post(pept2lca::post_json_handler_v1),
-        "/pept2prot",
-        get(pept2prot::get_json_handler).post(pept2prot::post_json_handler),
-        "/pept2taxa",
-        get(pept2taxa::get_json_handler_v1).post(pept2taxa::post_json_handler_v1),
-        "/peptinfo",
-        get(peptinfo::get_json_handler_v1).post(peptinfo::post_json_handler_v1),
-        "/protinfo",
-        get(protinfo::get_json_handler_v1).post(protinfo::post_json_handler_v1),
-        "/taxa2lca",
-        get(taxa2lca::get_json_handler_v1).post(taxa2lca::post_json_handler_v1),
-        "/taxa2tree",
-        get(taxa2tree::get_json_handler_v1).post(taxa2tree::post_json_handler_v1),
-        "/taxonomy",
-        get(taxonomy::get_json_handler_v1).post(taxonomy::post_json_handler_v1)
-    )
-    .route("/taxa2tree.html", get(taxa2tree::get_html_handler_v1).post(taxa2tree::post_html_handler_v1))
-}
-
 fn create_api_v2_routes() -> Router<AppState> {
     define_routes!(
         "/pept2ec",
diff --git a/datastore/src/lineage_store.rs b/datastore/src/lineage_store.rs
diff --git a/datastore/src/taxon_store.rs b/datastore/src/taxon_store.rs

Original file line number	Diff line number	Diff line change
`@@ -87,7 +87,7 @@ async fn handler(`
`87`	`87`	`}`
`88`	`88`
`89`	`89`	`generate_handlers! (`
`90`		`- [ V1, V2 ]`
	`90`	`+ [ V2 ]`
`91`	`91`	`async fn json_handler(`
`92`	`92`	`state => State<AppState>,`
`93`	`93`	`params => Parameters,`
Original file line number	Diff line number	Diff line change
`@@ -120,7 +120,7 @@ async fn handler(`
`120`	`120`	`}`
`121`	`121`
`122`	`122`	`generate_handlers! (`
`123`		`- [ V1, V2 ]`
	`123`	`+ [ V2 ]`
`124`	`124`	`async fn json_handler(`
`125`	`125`	`state => State<AppState>,`
`126`	`126`	`params => Parameters,`
Original file line number	Diff line number	Diff line change
`@@ -110,7 +110,7 @@ async fn handler(`
`110`	`110`	`}`
`111`	`111`
`112`	`112`	`generate_handlers! (`
`113`		`- [ V1, V2 ]`
	`113`	`+ [ V2 ]`
`114`	`114`	`async fn json_handler(`
`115`	`115`	`state => State<AppState>,`
`116`	`116`	`params => Parameters,`
Original file line number	Diff line number	Diff line change
`@@ -105,7 +105,7 @@ async fn handler(`
`105`	`105`	`}`
`106`	`106`
`107`	`107`	`generate_handlers! (`
`108`		`- [ V1, V2 ]`
	`108`	`+ [ V2 ]`
`109`	`109`	`async fn json_handler(`
`110`	`110`	`state => State<AppState>,`
`111`	`111`	`params => Parameters,`
Original file line number	Diff line number	Diff line change
`@@ -80,7 +80,7 @@ async fn handler(`
`80`	`80`	`}`
`81`	`81`
`82`	`82`	`generate_handlers! (`
`83`		`- [ V1, V2 ]`
	`83`	`+ [ V2 ]`
`84`	`84`	`async fn json_handler(`
`85`	`85`	`state => State<AppState>,`
`86`	`86`	`params => Parameters,`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-pub mod v1;`
`2`	`1`	`pub mod v2;`
`3`	`2`
`4`	`3`	`use datastore::{LineageStore, TaxonStore};`
`@@ -60,7 +59,7 @@ macro_rules! create_lineages {`
`60`	`59`
`61`	`60`	`pub fn get_lineage_array_numeric(taxon_id: u32, lineage_store: &LineageStore) -> Vec<i32> {`
`62`	`61`	`let lineage = lineage_store.get(taxon_id).cloned().unwrap_or_default();`
`63`		`-`
	`62`	`+`
`64`	`63`	`vec![`
`65`	`64`	`$(`
`66`	`65`	`get_id(lineage.$field).unwrap_or(0),`
`@@ -70,7 +69,7 @@ macro_rules! create_lineages {`
`70`	`69`
`71`	`70`	`pub fn get_lineage_with_names(taxon_id: u32, lineage_store: &LineageStore, taxon_store: &TaxonStore) -> Option<LineageWithNames> {`
`72`	`71`	`let lineage = lineage_store.get(taxon_id)?;`
`73`		`-`
	`72`	`+`
`74`	`73`	`Some(LineageWithNames {`
`75`	`74`	`$(`
`76`	`75`	`[<$field _id>]: get_id(lineage.$field),`
`@@ -96,83 +95,70 @@ pub(crate) use create_lineages;`
`96`	`95`
`97`	`96`	`#[derive(Clone, Copy)]`
`98`	`97`	`pub enum LineageVersion {`
`99`		`- V1,`
`100`	`98`	`V2`
`101`	`99`	`}`
`102`	`100`
`103`	`101`	`#[derive(Serialize, Debug)]`
`104`	`102`	`#[serde(untagged)]`
	`103`	`+#[allow(clippy::large_enum_variant)]`
`105`	`104`	`pub enum Lineage {`
`106`		`- DefaultV1(v1::Lineage),`
`107`		`- NamesV1(v1::LineageWithNames),`
`108`	`105`	`DefaultV2(v2::Lineage),`
`109`	`106`	`NamesV2(v2::LineageWithNames)`
`110`	`107`	`}`
`111`	`108`
`112`	`109`	`pub fn get_lineage(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Option<Lineage> {`
`113`	`110`	`match version {`
`114`		`- LineageVersion::V1 => v1::get_lineage(taxon_id, lineage_store).map(Lineage::DefaultV1),`
`115`	`111`	`LineageVersion::V2 => v2::get_lineage(taxon_id, lineage_store).map(Lineage::DefaultV2)`
`116`	`112`	`}`
`117`	`113`	`}`
`118`	`114`
`119`	`115`	`pub fn get_empty_lineage(version: LineageVersion) -> Option<Lineage> {`
`120`	`116`	`match version {`
`121`		`- LineageVersion::V1 => v1::get_empty_lineage().map(Lineage::DefaultV1),`
`122`	`117`	`LineageVersion::V2 => v2::get_empty_lineage().map(Lineage::DefaultV2)`
`123`	`118`	`}`
`124`	`119`	`}`
`125`	`120`
`126`	`121`	`pub fn get_lineage_array(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Vec<Option<i32>> {`
`127`	`122`	`match version {`
`128`		`- LineageVersion::V1 => v1::get_lineage_array(taxon_id, lineage_store),`
`129`	`123`	`LineageVersion::V2 => v2::get_lineage_array(taxon_id, lineage_store)`
`130`	`124`	`}`
`131`	`125`	`}`
`132`	`126`
`133`	`127`	`pub fn get_lineage_array_numeric(taxon_id: u32, version: LineageVersion, lineage_store: &LineageStore) -> Vec<i32> {`
`134`	`128`	`match version {`
`135`		`- LineageVersion::V1 => v1::get_lineage_array_numeric(taxon_id, lineage_store),`
`136`	`129`	`LineageVersion::V2 => v2::get_lineage_array_numeric(taxon_id, lineage_store)`
`137`	`130`	`}`
`138`	`131`	`}`
`139`	`132`
`140`	`133`	`pub fn get_lineage_with_names(`
`141`	`134`	`taxon_id: u32,`
`142`		`- version: LineageVersion,`
	`135`	`+ _version: LineageVersion,`
`143`	`136`	`lineage_store: &LineageStore,`
`144`	`137`	`taxon_store: &TaxonStore`
`145`	`138`	`) -> Option<Lineage> {`
`146`		`- match version {`
`147`		`- LineageVersion::V1 => v1::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV1),`
`148`		`- LineageVersion::V2 => v2::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV2)`
`149`		`- }`
	`139`	`+ v2::get_lineage_with_names(taxon_id, lineage_store, taxon_store).map(Lineage::NamesV2)`
`150`	`140`	`}`
`151`	`141`
`152`	`142`	`pub fn get_empty_lineage_with_names(version: LineageVersion) -> Option<Lineage> {`
`153`	`143`	`match version {`
`154`		`- LineageVersion::V1 => v1::get_empty_lineage_with_names().map(Lineage::NamesV1),`
`155`	`144`	`LineageVersion::V2 => v2::get_empty_lineage_with_names().map(Lineage::NamesV2)`
`156`	`145`	`}`
`157`	`146`	`}`
`158`	`147`
`159`	`148`	`pub fn get_amount_of_ranks(version: LineageVersion) -> u8 {`
`160`	`149`	`match version {`
`161`		`- LineageVersion::V1 => 28,`
`162`		`- LineageVersion::V2 => 27`
	`150`	`+ LineageVersion::V2 => 28`
`163`	`151`	`}`
`164`	`152`	`}`
`165`	`153`
`166`	`154`	`pub fn get_genus_index(version: LineageVersion) -> u8 {`
`167`	`155`	`match version {`
`168`		`- LineageVersion::V1 => 20,`
`169`		`- LineageVersion::V2 => 18`
	`156`	`+ LineageVersion::V2 => 19`
`170`	`157`	`}`
`171`	`158`	`}`
`172`	`159`
`173`	`160`	`pub fn get_species_index(version: LineageVersion) -> u8 {`
`174`	`161`	`match version {`
`175`		`- LineageVersion::V1 => 24,`
`176`		`- LineageVersion::V2 => 22`
	`162`	`+ LineageVersion::V2 => 23`
`177`	`163`	`}`
`178`	`164`	`}`