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

varfish-org · Oct 21, 2023 · 434edb2 · 434edb2
1 parent 0f42d20
commit 434edb2
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Showing 37 changed files with 10 additions and 143 deletions.
diff --git a/Cargo.toml b/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"

diff --git a/src/data/cdot/json.rs b/src/data/cdot/json.rs
@@ -10,8 +10,8 @@ use crate::{
         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 @@ 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)
     }
@@ -1082,7 +1082,7 @@ pub mod tests {
     };
     use crate::mapper::assembly::{self, Mapper};
     use crate::parser::HgvsVariant;
-    use crate::static_data::Assembly;
+    use biocommons_bioutils::assemblies::Assembly;
 
     #[test]
     fn test_sync() {

diff --git a/src/data/interface.rs b/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.
 ///

diff --git a/src/data/uta.rs b/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,

diff --git a/src/data/uta_sr.rs b/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)
     }

diff --git a/src/lib.rs b/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;
diff --git a/src/mapper/assembly.rs b/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 {

diff --git a/src/mapper/variant.rs b/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");
             }

diff --git a/src/static_data/_data/CHM1_1.0.json.gz b/src/static_data/_data/CHM1_1.0.json.gz
diff --git a/src/static_data/_data/CHM1_1.1.json.gz b/src/static_data/_data/CHM1_1.1.json.gz
diff --git a/src/static_data/_data/GRCh37.json.gz b/src/static_data/_data/GRCh37.json.gz
diff --git a/src/static_data/_data/GRCh37.p10.json.gz b/src/static_data/_data/GRCh37.p10.json.gz
diff --git a/src/static_data/_data/GRCh37.p11.json.gz b/src/static_data/_data/GRCh37.p11.json.gz
diff --git a/src/static_data/_data/GRCh37.p12.json.gz b/src/static_data/_data/GRCh37.p12.json.gz
diff --git a/src/static_data/_data/GRCh37.p13.json.gz b/src/static_data/_data/GRCh37.p13.json.gz
diff --git a/src/static_data/_data/GRCh37.p2.json.gz b/src/static_data/_data/GRCh37.p2.json.gz
diff --git a/src/static_data/_data/GRCh37.p5.json.gz b/src/static_data/_data/GRCh37.p5.json.gz
diff --git a/src/static_data/_data/GRCh37.p9.json.gz b/src/static_data/_data/GRCh37.p9.json.gz
diff --git a/src/static_data/_data/GRCh38.json.gz b/src/static_data/_data/GRCh38.json.gz
diff --git a/src/static_data/_data/GRCh38.p1.json.gz b/src/static_data/_data/GRCh38.p1.json.gz
diff --git a/src/static_data/_data/GRCh38.p10.json.gz b/src/static_data/_data/GRCh38.p10.json.gz
diff --git a/src/static_data/_data/GRCh38.p11.json.gz b/src/static_data/_data/GRCh38.p11.json.gz
diff --git a/src/static_data/_data/GRCh38.p12.json.gz b/src/static_data/_data/GRCh38.p12.json.gz
diff --git a/src/static_data/_data/GRCh38.p2.json.gz b/src/static_data/_data/GRCh38.p2.json.gz
diff --git a/src/static_data/_data/GRCh38.p3.json.gz b/src/static_data/_data/GRCh38.p3.json.gz
diff --git a/src/static_data/_data/GRCh38.p4.json.gz b/src/static_data/_data/GRCh38.p4.json.gz
diff --git a/src/static_data/_data/GRCh38.p5.json.gz b/src/static_data/_data/GRCh38.p5.json.gz
diff --git a/src/static_data/_data/GRCh38.p6.json.gz b/src/static_data/_data/GRCh38.p6.json.gz
diff --git a/src/static_data/_data/GRCh38.p7.json.gz b/src/static_data/_data/GRCh38.p7.json.gz
diff --git a/src/static_data/_data/GRCh38.p8.json.gz b/src/static_data/_data/GRCh38.p8.json.gz
diff --git a/src/static_data/_data/GRCh38.p9.json.gz b/src/static_data/_data/GRCh38.p9.json.gz
diff --git a/src/static_data/_data/Makefile b/src/static_data/_data/Makefile
diff --git a/src/static_data/_data/NCBI33.json.gz b/src/static_data/_data/NCBI33.json.gz
diff --git a/src/static_data/_data/NCBI34.json.gz b/src/static_data/_data/NCBI34.json.gz
diff --git a/src/static_data/_data/NCBI35.json.gz b/src/static_data/_data/NCBI35.json.gz
diff --git a/src/static_data/_data/NCBI36.json.gz b/src/static_data/_data/NCBI36.json.gz
diff --git a/src/static_data/mod.rs b/src/static_data/mod.rs