feat: move out assemblies to biocommons_bioutils crate (#134)

Cargo.toml

@@ -32,6 +32,7 @@ serde_json = "1.0"
 serde = { version = "1.0", features = ["derive"] }
 thiserror = "1.0"
 indexmap = { version = "2", features = ["serde"] }
+biocommons-bioutils = "0.1.0"
 
 [dev-dependencies]
 anyhow = "1.0"

src/data/cdot/json.rs

@@ -10,8 +10,8 @@
         self, GeneInfoRecord, TxExonsRecord, TxForRegionRecord, TxIdentityInfo, TxInfoRecord,
         TxMappingOptionsRecord, TxSimilarityRecord,
     },
-    static_data::{Assembly, ASSEMBLY_INFOS},
 };
+use biocommons_bioutils::assemblies::{Assembly, ASSEMBLY_INFOS};
 
 use bio::data_structures::interval_tree::ArrayBackedIntervalTree;
 use chrono::NaiveDateTime;
@@ -104,7 +104,7 @@
 
     fn get_assembly_map(
         &self,
-        assembly: crate::static_data::Assembly,
+        assembly: biocommons_bioutils::assemblies::Assembly,
     ) -> indexmap::IndexMap<String, String> {
         self.inner.get_assembly_map(assembly)
     }
@@ -625,7 +625,7 @@
                     .clone();
                 transcript_ids_for_gene
                     .entry(gene_symbol.clone())
                     .or_insert(Vec::new());
                 genes.insert(gene_symbol, gene.clone());
             });
         c_txs
@@ -1082,7 +1082,7 @@
     };
     use crate::mapper::assembly::{self, Mapper};
     use crate::parser::HgvsVariant;
-    use crate::static_data::Assembly;
+    use biocommons_bioutils::assemblies::Assembly;
 
     #[test]
     fn test_sync() {

src/data/interface.rs

@@ -4,7 +4,7 @@ use chrono::NaiveDateTime;
 use indexmap::IndexMap;
 
 use crate::data::error::Error;
-use crate::static_data::Assembly;
+use biocommons_bioutils::assemblies::Assembly;
 
 /// Information about a gene.
 ///

src/data/uta.rs

@@ -9,7 +9,7 @@ use std::fmt::Debug;
 use std::sync::Mutex;
 
 use crate::sequences::seq_md5;
-use crate::static_data::{Assembly, ASSEMBLY_INFOS};
+use biocommons_bioutils::assemblies::{Assembly, ASSEMBLY_INFOS};
 
 use crate::data::{
     error::Error, interface, interface::GeneInfoRecord, interface::TxExonsRecord,
@@ -604,8 +604,9 @@ impl interface::Provider for Provider {
 
 #[cfg(test)]
 mod test {
-    use crate::{data::interface::Provider as InterfaceProvider, static_data::Assembly};
+    use crate::data::interface::Provider as InterfaceProvider;
     use anyhow::Error;
+    use biocommons_bioutils::assemblies::Assembly;
 
     use super::{Config, Provider};
 

src/data/uta_sr.rs

@@ -92,7 +92,7 @@ impl interface::Provider for Provider {
 
     fn get_assembly_map(
         &self,
-        assembly: crate::static_data::Assembly,
+        assembly: biocommons_bioutils::assemblies::Assembly,
     ) -> indexmap::IndexMap<String, String> {
         self.inner.get_assembly_map(assembly)
     }

src/lib.rs

@@ -3,5 +3,4 @@ pub mod mapper;
 pub mod normalizer;
 pub mod parser;
 pub mod sequences;
-pub mod static_data;
 pub mod validator;

src/mapper/assembly.rs

@@ -8,7 +8,8 @@ use std::sync::Arc;
 use crate::mapper::error::Error;
 use crate::mapper::variant;
 use crate::parser::HgvsVariant;
-use crate::{data::interface::Provider, static_data::Assembly, validator::ValidationLevel};
+use crate::{data::interface::Provider, validator::ValidationLevel};
+use biocommons_bioutils::assemblies::Assembly;
 
 #[derive(Debug, PartialEq, Eq, Default, Clone, Copy)]
 pub enum InParAssume {
@@ -373,8 +374,9 @@ impl Mapper {
 
 #[cfg(test)]
 mod test {
-    use crate::{data::uta_sr::test_helpers::build_provider, static_data::Assembly};
+    use crate::data::uta_sr::test_helpers::build_provider;
     use anyhow::Error;
+    use biocommons_bioutils::assemblies::Assembly;
 
     use super::{Config, Mapper};
 

src/mapper/variant.rs

@@ -1152,7 +1152,7 @@ mod test {
 
             fn get_assembly_map(
                 &self,
-                _assembly: crate::static_data::Assembly,
+                _assembly: biocommons_bioutils::assemblies::Assembly,
             ) -> indexmap::IndexMap<String, String> {
                 panic!("for test use only");
             }