Merge pull request #296 from umccr/feat/crypt4gh-location

feat(config): add ability to specify simple locations with keys
umccr · Jan 22, 2025 · c259f73 · c259f73
2 parents 9dde560 + e4192b9
commit c259f73
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Showing 8 changed files with 49 additions and 10 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/htsget-config/Cargo.toml b/htsget-config/Cargo.toml
@@ -12,7 +12,7 @@ repository = "https://github.com/umccr/htsget-rs"
 
 [features]
 aws = ["dep:aws-sdk-secretsmanager", "dep:aws-config", "dep:tempfile"]
-url = ["dep:reqwest", "dep:cfg-if"]
+url = ["dep:reqwest"]
 experimental = ["dep:crypt4gh", "dep:tokio", "dep:futures-util"]
 default = []
 
@@ -25,6 +25,7 @@ serde_with = "3"
 serde_json = "1"
 serde_regex = "1"
 regex = "1"
+cfg-if = { version = "1" }
 figment = { version = "0.10", features = ["env", "toml"] }
 clap = { version = "4", features = ["derive", "env", "cargo"] }
 tracing = "0.1"
@@ -39,7 +40,6 @@ chrono = { version = "0.4", features = ["now"], default-features = false }
 
 # url
 reqwest = { version = "0.12", features = ["rustls-tls"], default-features = false, optional = true }
-cfg-if = { version = "1", optional = true }
 
 # Crypt4GH
 crypt4gh = { version = "0.4", git = "https://github.com/EGA-archive/crypt4gh-rust", optional = true }

diff --git a/htsget-config/src/config/advanced/url.rs b/htsget-config/src/config/advanced/url.rs
@@ -118,7 +118,9 @@ impl TryFrom<Url> for storage::url::Url {
 
     cfg_if! {
       if #[cfg(feature = "experimental")] {
-        Ok(url_storage.set_keys(storage.keys))
+        let mut url_storage = url_storage;
+        url_storage.set_keys(storage.keys);
+        Ok(url_storage)
       } else {
         Ok(url_storage)
       }

diff --git a/htsget-config/src/config/location.rs b/htsget-config/src/config/location.rs
@@ -4,9 +4,12 @@
 use crate::config::advanced::regex_location::RegexLocation;
 use crate::error::{Error::ParseError, Result};
 use crate::storage;
+#[cfg(feature = "experimental")]
+use crate::storage::c4gh::C4GHKeys;
 use crate::storage::file::default_authority;
 use crate::storage::Backend;
 use crate::types::Scheme;
+use cfg_if::cfg_if;
 use serde::de::Error;
 use serde::{Deserialize, Deserializer, Serialize};
 use std::result;
@@ -130,6 +133,17 @@ impl From<LocationsOneOrMany> for Locations {
   }
 }
 
+/// Deserialize into a string location that also supports setting additional fields
+/// for the backend.
+#[derive(Serialize, Deserialize, Debug, Clone, Default)]
+#[serde(default, deny_unknown_fields)]
+struct ExtendedLocation {
+  location: StringLocation,
+  #[cfg(feature = "experimental")]
+  #[serde(skip_serializing)]
+  keys: Option<C4GHKeys>,
+}
+
 /// Deserialize the location from a string with a protocol.
 #[derive(Serialize, Debug, Clone, Default)]
 #[serde(default, deny_unknown_fields)]
@@ -159,13 +173,25 @@ struct MapLocation {
 enum LocationWrapper {
   String(StringLocation),
   Map(MapLocation),
+  Extended(ExtendedLocation),
 }
 
 impl From<LocationWrapper> for Location {
   fn from(location: LocationWrapper) -> Self {
     match location {
       LocationWrapper::String(location) => Location::new(location.backend, location.prefix),
       LocationWrapper::Map(location) => Location::new(location.backend, location.prefix),
+      LocationWrapper::Extended(location) => {
+        cfg_if! {
+          if #[cfg(feature = "experimental")] {
+            let mut location = location;
+            location.location.backend.set_keys(location.keys);
+            Location::new(location.location.backend, location.location.prefix)
+          } else {
+            Location::new(location.location.backend, location.location.prefix)
+          }
+        }
+      }
     }
   }
 }

diff --git a/htsget-config/src/storage/file.rs b/htsget-config/src/storage/file.rs
@@ -55,9 +55,8 @@ impl File {
 
   #[cfg(feature = "experimental")]
   /// Set the C4GH keys.
-  pub fn set_keys(mut self, keys: Option<C4GHKeys>) -> Self {
+  pub fn set_keys(&mut self, keys: Option<C4GHKeys>) {
     self.keys = keys;
-    self
   }
 
   #[cfg(feature = "experimental")]

diff --git a/htsget-config/src/storage/mod.rs b/htsget-config/src/storage/mod.rs
@@ -4,6 +4,8 @@
 #[cfg(any(feature = "url", feature = "aws"))]
 use crate::error::Error;
 use crate::error::Result;
+#[cfg(feature = "experimental")]
+use crate::storage::c4gh::C4GHKeys;
 use crate::storage::file::File;
 #[cfg(feature = "aws")]
 use crate::storage::s3::S3;
@@ -81,6 +83,18 @@ impl Backend {
       Err(Error::ParseError("not a `File` variant".to_string()))
     }
   }
+
+  /// Set the C4GH keys.
+  #[cfg(feature = "experimental")]
+  pub fn set_keys(&mut self, keys: Option<C4GHKeys>) {
+    match self {
+      Backend::File(file) => file.set_keys(keys),
+      #[cfg(feature = "aws")]
+      Backend::S3(s3) => s3.set_keys(keys),
+      #[cfg(feature = "url")]
+      Backend::Url(url) => url.set_keys(keys),
+    }
+  }
 }
 
 impl Default for Backend {

diff --git a/htsget-config/src/storage/s3.rs b/htsget-config/src/storage/s3.rs
@@ -64,9 +64,8 @@ impl S3 {
 
   #[cfg(feature = "experimental")]
   /// Set the C4GH keys.
-  pub fn with_keys(mut self, keys: Option<C4GHKeys>) -> Self {
+  pub fn set_keys(&mut self, keys: Option<C4GHKeys>) {
     self.keys = keys;
-    self
   }
 
   #[cfg(feature = "experimental")]

diff --git a/htsget-config/src/storage/url.rs b/htsget-config/src/storage/url.rs
@@ -72,9 +72,8 @@ impl Url {
 
   #[cfg(feature = "experimental")]
   /// Set the C4GH keys.
-  pub fn set_keys(mut self, keys: Option<C4GHKeys>) -> Self {
+  pub fn set_keys(&mut self, keys: Option<C4GHKeys>) {
     self.keys = keys;
-    self
   }
 
   #[cfg(feature = "experimental")]