refactor: replace linked-hash-map by indexmap (#111) (#112)

Release-As: 0.8.2
varfish-org · Jun 8, 2023 · f6d3ab4 · f6d3ab4
1 parent 1a040e7
commit f6d3ab4
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Showing 6 changed files with 19 additions and 19 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -20,7 +20,6 @@ chrono = "0.4"
 enum-map = "2.4"
 flate2 = "1.0"
 lazy_static = "1.4"
-linked-hash-map = { version = "0.5", features = ["serde", "serde_impl"] }
 log = "0.4"
 md-5 = "0.10"
 nom = "7.1"
@@ -29,18 +28,19 @@ quick_cache = "0.3"
 regex = "1.7"
 rustc-hash = "1.1"
 seqrepo = { version = "0.5" }
-serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
+serde = { version = "1.0", features = ["derive"] }
 thiserror = "1.0"
+indexmap = { version = "1.9.3", features = ["serde"] }
 
 [dev-dependencies]
+anyhow = "1.0"
+criterion = "0.5"
 csv = "1.2"
 env_logger = "0.10"
 pretty_assertions = "1.3"
 rstest = "0.17"
 test-log = "0.2"
-criterion = "0.5"
-anyhow = "1.0"
 
 [[bench]]
 name = "translate_cds"

diff --git a/src/data/cdot/json.rs b/src/data/cdot/json.rs
@@ -15,7 +15,7 @@ use crate::{
 
 use bio::data_structures::interval_tree::ArrayBackedIntervalTree;
 use chrono::NaiveDateTime;
-use linked_hash_map::LinkedHashMap;
+use indexmap::IndexMap;
 use seqrepo::{Interface as SeqRepoInterface, SeqRepo};
 
 /// Configurationf or the `data::cdot::Provider`.
@@ -105,7 +105,7 @@ impl ProviderInterface for Provider {
     fn get_assembly_map(
         &self,
         assembly: crate::static_data::Assembly,
-    ) -> linked_hash_map::LinkedHashMap<String, String> {
+    ) -> indexmap::IndexMap<String, String> {
         self.inner.get_assembly_map(assembly)
     }
 
@@ -187,16 +187,16 @@ impl ProviderInterface for Provider {
 
 /// Data structures used for deserializing from cdot.
 pub mod models {
-    use linked_hash_map::LinkedHashMap;
+    use indexmap::IndexMap;
     use serde::{Deserialize, Deserializer};
 
     /// Container for a cDot data file.
     #[derive(Deserialize, Debug, Clone)]
     pub struct Container {
-        pub transcripts: LinkedHashMap<String, Transcript>,
+        pub transcripts: IndexMap<String, Transcript>,
         pub cdot_version: String,
         pub genome_builds: Vec<String>,
-        pub genes: LinkedHashMap<String, Gene>,
+        pub genes: IndexMap<String, Gene>,
     }
 
     /// Enum for representing the tags for transcripts.
@@ -221,7 +221,7 @@ pub mod models {
         /// `"ENSG00000012048"` for BRCA1.
         pub gene_version: String,
         /// Alignments to the different genome builds.
-        pub genome_builds: LinkedHashMap<String, GenomeAlignment>,
+        pub genome_builds: IndexMap<String, GenomeAlignment>,
         /// HGNC identifier, e.g. `"1100"` for BRCA1 which is `HGNC:1100`.
         #[serde(default)]
         pub hgnc: Option<String>,
@@ -709,8 +709,8 @@ impl TxProvider {
         REQUIRED_VERSION
     }
 
-    fn get_assembly_map(&self, assembly: Assembly) -> LinkedHashMap<String, String> {
-        LinkedHashMap::from_iter(
+    fn get_assembly_map(&self, assembly: Assembly) -> IndexMap<String, String> {
+        IndexMap::from_iter(
             ASSEMBLY_INFOS[assembly]
                 .sequences
                 .iter()

diff --git a/src/data/interface.rs b/src/data/interface.rs
@@ -1,7 +1,7 @@
 //! Definition of the interface for accessing the transcript database.
 
 use chrono::NaiveDateTime;
-use linked_hash_map::LinkedHashMap;
+use indexmap::IndexMap;
 
 use crate::data::error::Error;
 use crate::static_data::Assembly;
@@ -193,7 +193,7 @@ pub trait Provider {
     /// # Arguments
     ///
     /// * `assembly` - The assembly to build the map for.
-    fn get_assembly_map(&self, assembly: Assembly) -> LinkedHashMap<String, String>;
+    fn get_assembly_map(&self, assembly: Assembly) -> IndexMap<String, String>;
 
     /// Returns the basic information about the gene.
     ///

diff --git a/src/data/uta.rs b/src/data/uta.rs
@@ -2,7 +2,7 @@
 //!
 //! C.f. https://github.com/biocommons/uta
 
-use linked_hash_map::LinkedHashMap;
+use indexmap::IndexMap;
 use postgres::{Client, NoTls, Row};
 use quick_cache::sync::Cache;
 use std::fmt::Debug;
@@ -243,8 +243,8 @@ impl ProviderInterface for Provider {
         &self.schema_version
     }
 
-    fn get_assembly_map(&self, assembly: Assembly) -> LinkedHashMap<String, String> {
-        LinkedHashMap::from_iter(
+    fn get_assembly_map(&self, assembly: Assembly) -> IndexMap<String, String> {
+        IndexMap::from_iter(
             ASSEMBLY_INFOS[assembly]
                 .sequences
                 .iter()

diff --git a/src/data/uta_sr.rs b/src/data/uta_sr.rs
@@ -93,7 +93,7 @@ impl ProviderInterface for Provider {
     fn get_assembly_map(
         &self,
         assembly: crate::static_data::Assembly,
-    ) -> linked_hash_map::LinkedHashMap<String, String> {
+    ) -> indexmap::IndexMap<String, String> {
         self.inner.get_assembly_map(assembly)
     }
 

diff --git a/src/mapper/variant.rs b/src/mapper/variant.rs
@@ -1134,7 +1134,7 @@ mod test {
             fn get_assembly_map(
                 &self,
                 _assembly: crate::static_data::Assembly,
-            ) -> linked_hash_map::LinkedHashMap<String, String> {
+            ) -> indexmap::IndexMap<String, String> {
                 panic!("for test use only");
             }