Resource

.github/workflows/check.yml

@@ -43,6 +43,8 @@ jobs:
 
   clippy-stable:
     runs-on: ubuntu-latest
+    env:
+      RUST_VERSION: "1.98.0"
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -59,20 +61,20 @@ jobs:
             ~/.cargo/git/db/
             ~/.rustup/toolchains/
             target/
-          key: ${{ runner.os }}-cargo-check-stable-${{ hashFiles('**/Cargo.lock') }}
+          key: ${{ runner.os }}-cargo-check-${{ env.RUST_VERSION }}-${{ hashFiles('**/Cargo.lock') }}
 
       - name: Install stable toolchain
-        run: rustup toolchain install stable
+        run: rustup toolchain install ${{ env.RUST_VERSION }} --component clippy
 
       - name: Install WASM toolchain
-        run: rustup target add wasm32-unknown-unknown --toolchain stable
+        run: rustup target add wasm32-unknown-unknown --toolchain ${{ env.RUST_VERSION }}
 
       - name: Check on stable
-        run: cargo +stable clippy --all-targets -p utile -p puv -- -D warnings
+        run: cargo +${{ env.RUST_VERSION }} clippy --all-targets -p utile -p puv -- -D warnings
 
       - name: Check project (WASM) on stable
         # Note lack of --all-targets here because tests and examples are not wasm compatible
-        run: cargo +stable clippy --target wasm32-unknown-unknown -p utile -p puv -- -D warnings
+        run: cargo +${{ env.RUST_VERSION }} clippy --target wasm32-unknown-unknown -p utile -p puv -- -D warnings
 
   test:
     runs-on: ubuntu-latest

ensembl/src/contig/grch37_meta.rs

@@ -94,7 +94,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::resource::EnsemblResource;
 

ensembl/src/contig/grch38_meta.rs

@@ -715,7 +715,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::resource::EnsemblResource;
 

ensembl/src/resource.rs

@@ -1,5 +1,5 @@
+use resource::{ReadResource, Resource, UrlResource};
 use url::Url;
-use resource::{RawResource, UrlResource};
 
 const GRCH38_REFERENCE_GENOME_INDEXED: &str =
     "fasta/homo_sapiens/dna_index/Homo_sapiens.GRCh38.dna.toplevel.fa.gz";
@@ -106,7 +106,7 @@ impl EnsemblResource {
         UrlResource::new(self.url()).unwrap()
     }
 }
-impl RawResource for EnsemblResource {
+impl Resource for EnsemblResource {
     const NAMESPACE: &'static str = "ensembl";
 
     fn key(&self) -> String {
@@ -116,16 +116,17 @@ impl RawResource for EnsemblResource {
     fn compression(&self) -> Option<resource::Compression> {
         resource::Compression::infer(&self.key)
     }
-
-    type Reader = <UrlResource as RawResource>::Reader;
+}
+impl ReadResource for EnsemblResource {
+    type Reader = <UrlResource as ReadResource>::Reader;
     fn size(&self) -> std::io::Result<u64> {
         self.url_resource().size()
     }
     fn read(&self) -> std::io::Result<Self::Reader> {
         self.url_resource().read()
     }
 
-    type AsyncReader = <UrlResource as RawResource>::AsyncReader;
+    type AsyncReader = <UrlResource as ReadResource>::AsyncReader;
     async fn size_async(&self) -> std::io::Result<u64> {
         self.url_resource().size_async().await
     }

genomes1000/examples/load_all.rs

@@ -1,4 +1,4 @@
-use resource::RawResourceExt;
+use resource::ResourceExt;
 
 use genomes1000::{GRCh38Contig, load_grch38_reference_genome, source::Genomes1000Resource};
 

genomes1000/src/contig/grch37_meta.rs

@@ -101,7 +101,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::source::Genomes1000Resource;
 

genomes1000/src/contig/grch38_meta.rs

@@ -3388,7 +3388,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::source::Genomes1000Resource;
 

genomes1000/src/lib.rs

@@ -19,7 +19,7 @@ use biocore::{
     location::{ContigPosition, ContigRange},
     vcf::IndexedVcfReader,
 };
-use resource::{RawResource, RawResourceExt, fs::FsCache};
+use resource::{ReadResource, ResourceExt, cache::fs::FsCache};
 use utile::{io::FromUtf8Bytes, iter::IteratorExt};
 
 use self::{pedigree::Pedigree, simplified::SimplifiedRecord, source::Genomes1000Resource};
@@ -435,7 +435,7 @@ pub async fn load_contig(
     parse::parse(resource.read()?, sample_reading_function(c))
 }
 
-pub async fn load_pedigree(resource: impl RawResource) -> io::Result<Vec<Pedigree>> {
+pub async fn load_pedigree(resource: impl ReadResource) -> io::Result<Vec<Pedigree>> {
     Ok(csv::ReaderBuilder::new()
         .delimiter(b' ')
         .from_reader(resource.read()?)
@@ -458,11 +458,11 @@ pub async fn load_pedigree(resource: impl RawResource) -> io::Result<Vec<Pedigre
 /// It should also implement [Seek](std::io::Seek) if random access is needed.
 pub async fn load_grch38_reference_genome<F>(
     fasta: F,
-    index: impl RawResource,
+    index: impl ReadResource,
 ) -> io::Result<biocore::fasta::IndexedFastaReader<F::Reader>>
 where
-    F: RawResource,
-    <F as RawResource>::Reader: std::io::BufRead,
+    F: ReadResource,
+    <F as ReadResource>::Reader: std::io::BufRead,
 {
     biocore::fasta::IndexedFastaReader::new(fasta.read()?, index.decompressed().buffered().read()?)
 }
@@ -471,11 +471,11 @@ where
 /// It should also implement [Seek](std::io::Seek) if random access is needed.
 pub async fn load_grch37_reference_genome<F>(
     fasta: F,
-    index: impl RawResource,
+    index: impl ReadResource,
 ) -> io::Result<biocore::fasta::IndexedFastaReader<F::Reader>>
 where
-    F: RawResource,
-    <F as RawResource>::Reader: std::io::BufRead,
+    F: ReadResource,
+    <F as ReadResource>::Reader: std::io::BufRead,
 {
     biocore::fasta::IndexedFastaReader::new(fasta.read()?, index.decompressed().buffered().read()?)
 }

genomes1000/src/slow.rs

@@ -1,4 +1,4 @@
-use resource::{RawResource, RawResourceExt};
+use resource::{ReadResource, ResourceExt};
 use std::{collections::HashMap, io::Read};
 
 use crate::source::Genomes1000Resource;

genomes1000/src/source.rs

@@ -1,4 +1,4 @@
-use resource::{RawResource, UrlResource};
+use resource::{ReadResource, Resource, UrlResource};
 use url::Url;
 
 use crate::contig::GRCh38Contig;
@@ -158,7 +158,7 @@ impl Genomes1000Resource {
         UrlResource::new(self.url()).unwrap()
     }
 }
-impl RawResource for Genomes1000Resource {
+impl Resource for Genomes1000Resource {
     const NAMESPACE: &'static str = "1000genomes";
 
     fn key(&self) -> String {
@@ -172,16 +172,17 @@ impl RawResource for Genomes1000Resource {
             resource::Compression::infer(&self.key)
         }
     }
-
-    type Reader = <UrlResource as RawResource>::Reader;
+}
+impl ReadResource for Genomes1000Resource {
+    type Reader = <UrlResource as ReadResource>::Reader;
     fn size(&self) -> std::io::Result<u64> {
         self.url_resource().size()
     }
     fn read(&self) -> std::io::Result<Self::Reader> {
         self.url_resource().read()
     }
 
-    type AsyncReader = <UrlResource as RawResource>::AsyncReader;
+    type AsyncReader = <UrlResource as ReadResource>::AsyncReader;
     async fn size_async(&self) -> std::io::Result<u64> {
         self.url_resource().size_async().await
     }

gwas_catalog/src/lib.rs

@@ -5,7 +5,7 @@ use serde::{Deserialize, Serialize};
 use url::Url;
 
 use biocore::location::ContigPosition;
-use resource::{RawResource, RawResourceExt, UrlResource};
+use resource::{ReadResource, Resource, ResourceExt, UrlResource};
 use utile::io::reqwest_error;
 
 #[derive(Debug, Clone, PartialEq, Eq, Hash)]
@@ -39,7 +39,7 @@ impl GwasCatalogResource {
         Self::ANCESTRY_URL.parse().unwrap()
     }
 }
-impl RawResource for GwasCatalogResource {
+impl Resource for GwasCatalogResource {
     const NAMESPACE: &'static str = "gwas_catalog";
 
     fn key(&self) -> String {
@@ -49,8 +49,9 @@ impl RawResource for GwasCatalogResource {
     fn compression(&self) -> Option<resource::Compression> {
         None
     }
-
-    type Reader = <UrlResource as RawResource>::Reader;
+}
+impl ReadResource for GwasCatalogResource {
+    type Reader = <UrlResource as ReadResource>::Reader;
     fn size(&self) -> std::io::Result<u64> {
         Ok(self.size)
     }
@@ -59,7 +60,7 @@ impl RawResource for GwasCatalogResource {
         UrlResource::new(self.url).unwrap().read()
     }
 
-    type AsyncReader = <UrlResource as RawResource>::AsyncReader;
+    type AsyncReader = <UrlResource as ReadResource>::AsyncReader;
     async fn size_async(&self) -> std::io::Result<u64> {
         Ok(self.size)
     }

hail/src/contig/grch37_meta.rs

@@ -93,7 +93,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::source::HailCommonResource;
 

hail/src/contig/grch38_meta.rs

@@ -3375,7 +3375,7 @@ pub static META: phf::Map<&'static str, ContigMeta> = phf::phf_map! {
 
 #[cfg(test)]
 mod tests {
-    use resource::{RawResource, RawResourceExt};
+    use resource::{ReadResource, ResourceExt};
 
     use crate::source::HailCommonResource;
 

hail/src/lib.rs

@@ -3,7 +3,7 @@
 pub mod contig;
 pub mod source;
 
-use resource::{RawResource, RawResourceExt};
+use resource::{ReadResource, ResourceExt};
 use source::HailCommonResource;
 
 pub async fn load_grch38_reference_genome()

hail/src/source.rs

@@ -1,4 +1,4 @@
-use resource::{RawResource, UrlResource};
+use resource::{ReadResource, Resource, UrlResource};
 use url::Url;
 
 const HAIL_COMMON_BUCKET: &str = "hail-common";
@@ -44,7 +44,7 @@ impl HailCommonResource {
         UrlResource::new(self.url()).unwrap()
     }
 }
-impl RawResource for HailCommonResource {
+impl Resource for HailCommonResource {
     const NAMESPACE: &'static str = "hail_common";
 
     fn key(&self) -> String {
@@ -63,16 +63,17 @@ impl RawResource for HailCommonResource {
             _ => resource::Compression::infer_strict(&self.key),
         }
     }
-
-    type Reader = <UrlResource as RawResource>::Reader;
+}
+impl ReadResource for HailCommonResource {
+    type Reader = <UrlResource as ReadResource>::Reader;
     fn size(&self) -> std::io::Result<u64> {
         self.url_resource().size()
     }
     fn read(&self) -> std::io::Result<Self::Reader> {
         self.url_resource().read()
     }
 
-    type AsyncReader = <UrlResource as RawResource>::AsyncReader;
+    type AsyncReader = <UrlResource as ReadResource>::AsyncReader;
     async fn size_async(&self) -> std::io::Result<u64> {
         self.url_resource().size_async().await
     }

liftover/examples/load_all.rs

@@ -2,7 +2,7 @@ use liftover::{
     Liftover,
     sources::{EnsemblHG, EnsemblResource, UcscHG, UcscResource},
 };
-use resource::RawResourceExt;
+use resource::ResourceExt;
 
 #[tokio::main]
 async fn main() -> anyhow::Result<()> {

liftover/src/parse.rs

@@ -8,18 +8,18 @@ use std::{
 };
 
 use biocore::{genome::ArcContig, location::orientation::Stranded};
-use resource::{RawResource, RawResourceExt};
+use resource::{ReadResource, ResourceExt};
 use utile::io::read_ext::AsyncReadInto;
 
 use super::{
     AlignmentBlock, Chain, ChainHeader, ChainRange, ContigRange, Liftover, SequenceOrientation,
 };
 
 impl Liftover<ArcContig, ArcContig> {
-    pub fn load(resource: impl RawResource) -> anyhow::Result<Self> {
+    pub fn load(resource: impl ReadResource) -> anyhow::Result<Self> {
         Ok(Self::read(resource.decompressed().buffered().read()?)?)
     }
-    pub async fn load_async(resource: impl RawResource) -> anyhow::Result<Self> {
+    pub async fn load_async(resource: impl ReadResource) -> anyhow::Result<Self> {
         Ok(Self::read(
             &*resource
                 .decompressed()