From 434edb21e439f2d3edb6703cfc63be15858d90ad Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Sat, 21 Oct 2023 18:34:14 +0200 Subject: [PATCH 1/2] feat: move out assemblies to biocommons_bioutils crate (#134) --- Cargo.toml | 1 + src/data/cdot/json.rs | 6 +- src/data/interface.rs | 2 +- src/data/uta.rs | 2 +- src/data/uta_sr.rs | 2 +- src/lib.rs | 1 - src/mapper/assembly.rs | 3 +- src/mapper/variant.rs | 2 +- src/static_data/_data/CHM1_1.0.json.gz | Bin 25606 -> 0 bytes src/static_data/_data/CHM1_1.1.json.gz | Bin 719 -> 0 bytes src/static_data/_data/GRCh37.json.gz | Bin 2202 -> 0 bytes src/static_data/_data/GRCh37.p10.json.gz | Bin 5345 -> 0 bytes src/static_data/_data/GRCh37.p11.json.gz | Bin 5450 -> 0 bytes src/static_data/_data/GRCh37.p12.json.gz | Bin 5569 -> 0 bytes src/static_data/_data/GRCh37.p13.json.gz | Bin 5772 -> 0 bytes src/static_data/_data/GRCh37.p2.json.gz | Bin 3469 -> 0 bytes src/static_data/_data/GRCh37.p5.json.gz | Bin 4057 -> 0 bytes src/static_data/_data/GRCh37.p9.json.gz | Bin 4865 -> 0 bytes src/static_data/_data/GRCh38.json.gz | Bin 9194 -> 0 bytes src/static_data/_data/GRCh38.p1.json.gz | Bin 9533 -> 0 bytes src/static_data/_data/GRCh38.p10.json.gz | Bin 11093 -> 0 bytes src/static_data/_data/GRCh38.p11.json.gz | Bin 11430 -> 0 bytes src/static_data/_data/GRCh38.p12.json.gz | Bin 11789 -> 0 bytes src/static_data/_data/GRCh38.p2.json.gz | Bin 9789 -> 0 bytes src/static_data/_data/GRCh38.p3.json.gz | Bin 9928 -> 0 bytes src/static_data/_data/GRCh38.p4.json.gz | Bin 10212 -> 0 bytes src/static_data/_data/GRCh38.p5.json.gz | Bin 10351 -> 0 bytes src/static_data/_data/GRCh38.p6.json.gz | Bin 10419 -> 0 bytes src/static_data/_data/GRCh38.p7.json.gz | Bin 10496 -> 0 bytes src/static_data/_data/GRCh38.p8.json.gz | Bin 10817 -> 0 bytes src/static_data/_data/GRCh38.p9.json.gz | Bin 10976 -> 0 bytes src/static_data/_data/Makefile | 36 --------- src/static_data/_data/NCBI33.json.gz | Bin 2390 -> 0 bytes src/static_data/_data/NCBI34.json.gz | Bin 2468 -> 0 bytes src/static_data/_data/NCBI35.json.gz | Bin 1890 -> 0 bytes src/static_data/_data/NCBI36.json.gz | Bin 2009 -> 0 bytes src/static_data/mod.rs | 98 ----------------------- 37 files changed, 10 insertions(+), 143 deletions(-) delete mode 100644 src/static_data/_data/CHM1_1.0.json.gz delete mode 100644 src/static_data/_data/CHM1_1.1.json.gz delete mode 100644 src/static_data/_data/GRCh37.json.gz delete mode 100644 src/static_data/_data/GRCh37.p10.json.gz delete mode 100644 src/static_data/_data/GRCh37.p11.json.gz delete mode 100644 src/static_data/_data/GRCh37.p12.json.gz delete mode 100644 src/static_data/_data/GRCh37.p13.json.gz delete mode 100644 src/static_data/_data/GRCh37.p2.json.gz delete mode 100644 src/static_data/_data/GRCh37.p5.json.gz delete mode 100644 src/static_data/_data/GRCh37.p9.json.gz delete mode 100644 src/static_data/_data/GRCh38.json.gz delete mode 100644 src/static_data/_data/GRCh38.p1.json.gz delete mode 100644 src/static_data/_data/GRCh38.p10.json.gz delete mode 100644 src/static_data/_data/GRCh38.p11.json.gz delete mode 100644 src/static_data/_data/GRCh38.p12.json.gz delete mode 100644 src/static_data/_data/GRCh38.p2.json.gz delete mode 100644 src/static_data/_data/GRCh38.p3.json.gz delete mode 100644 src/static_data/_data/GRCh38.p4.json.gz delete mode 100644 src/static_data/_data/GRCh38.p5.json.gz delete mode 100644 src/static_data/_data/GRCh38.p6.json.gz delete mode 100644 src/static_data/_data/GRCh38.p7.json.gz delete mode 100644 src/static_data/_data/GRCh38.p8.json.gz delete mode 100644 src/static_data/_data/GRCh38.p9.json.gz delete mode 100644 src/static_data/_data/Makefile delete mode 100644 src/static_data/_data/NCBI33.json.gz delete mode 100644 src/static_data/_data/NCBI34.json.gz delete mode 100644 src/static_data/_data/NCBI35.json.gz delete mode 100644 src/static_data/_data/NCBI36.json.gz delete mode 100644 src/static_data/mod.rs diff --git a/Cargo.toml b/Cargo.toml index 211719c..bccc23b 100644 --- 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 index 12ae1f8..995c9c6 100644 --- 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 { 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 index 1a4dda3..f989990 100644 --- 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 index e9d7657..24822f0 100644 --- 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 index f12fcea..67d9750 100644 --- 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 { self.inner.get_assembly_map(assembly) } diff --git a/src/lib.rs b/src/lib.rs index 99e4f0c..bfd7d74 100644 --- 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 index 586b32b..4bd3c11 100644 --- 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 index 103c8a8..565b88c 100644 --- 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 { 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 deleted file mode 100644 index e6f4ed0d60a22f1aa844464730e804f803375969..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 25606 zcmYH^c_38#_fc91EtXQ2RLV$NOl9AaeVZ96kypKn(L#|SyP~Klq-e%A8kZ>FOi4nP 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GzDecoder::new(payload); - let mut grch37_json = String::new(); - d.read_to_string(&mut grch37_json) - .expect("should not happen; invalid gzip in embedded data"); - serde_json::from_str::(&grch37_json) - .expect("should not happen; invalid JSON in embedded data") - } -} - -#[derive(Debug, Deserialize)] -pub struct Sequence { - pub aliases: Vec, - pub assembly_unit: String, - pub genbank_ac: String, - pub length: usize, - pub name: String, - pub refseq_ac: String, - pub relationship: String, - pub sequence_role: String, -} - -#[derive(Debug, Deserialize)] -pub struct AssemblyInfo { - pub date: String, - pub description: String, - pub genbank_ac: String, - pub name: String, - pub refseq_ac: String, - pub sequences: Vec, - pub submitter: String, -} - -lazy_static::lazy_static! { - /// Provide information about the assemblies. - pub static ref ASSEMBLY_INFOS: EnumMap = enum_map! { - Assembly::Grch37 => Assembly::Grch37.load_assembly_info(), - Assembly::Grch37p10 => Assembly::Grch37p10.load_assembly_info(), - Assembly::Grch38 => Assembly::Grch38.load_assembly_info(), - }; -} - -#[cfg(test)] -mod test { - use pretty_assertions::assert_eq; - - use crate::static_data::{Assembly, ASSEMBLY_INFOS}; - - #[test] - fn smoke() { - assert_eq!(ASSEMBLY_INFOS[Assembly::Grch37].sequences.len(), 92); - assert_eq!(ASSEMBLY_INFOS[Assembly::Grch37p10].sequences.len(), 275); - assert_eq!(ASSEMBLY_INFOS[Assembly::Grch38].sequences.len(), 455); - } -} - -// -// Copyright 2023 hgvs-rs Contributors -// Copyright 2014 Bioutils Contributors -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// From 846721e96ef793b157b0031ca860addf603ad109 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Sat, 21 Oct 2023 18:42:22 +0200 Subject: [PATCH 2/2] wip --- src/data/uta.rs | 3 ++- src/mapper/assembly.rs | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/data/uta.rs b/src/data/uta.rs index 24822f0..91141b4 100644 --- a/src/data/uta.rs +++ b/src/data/uta.rs @@ -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}; diff --git a/src/mapper/assembly.rs b/src/mapper/assembly.rs index 4bd3c11..b1de930 100644 --- a/src/mapper/assembly.rs +++ b/src/mapper/assembly.rs @@ -374,8 +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};