cleaning up the codebase

Cargo.toml

@@ -48,49 +48,52 @@ mediator-coordination = { path = "./crates/web-plugins/didcomm-messaging/protoco
 # Other common dependencies
 serde = "1.0"
 sha2 = "0.10"
-cfg-if = "0.1"
+cfg-if = "1.0"
 getrandom = "0.2"
-hyper-tls = "0.5.0"
-json-patch = "1.0.0"
-x25519-dalek = "2.0.0-rc.3"
-multibase = "0.8.0"
+hyper-tls = "0.6.0"
+json-patch = "3.0.1"
+x25519-dalek = "2.0.1"
+multibase = "0.9.1"
 json-canon = "0.1.3"
-qrcode = "0.12.0"
-image = "0.23"
-reqwest = "0.11"
+qrcode = "0.14.1"
+image = "0.25"
+reqwest = "0.12"
 tempdir = "0.3.7"
-headers = "0.3"
-thiserror = "1.0.48"
-url = "2.4.1"
-num-bigint = "0.4.4"
-base64 = "0.13.0"
+headers = "0.4"
+thiserror = "2.0.7"
+url = "2.5.4"
+num-bigint = "0.4.6"
+base64 = "0.22.1"
 hex = "0.4.3"
 eyre = "0.6"
 anyhow = "1"
-subtle = "2.5.0"
-regex = "1.10.2"
-mongodb = "2.7.1"
-once_cell = "1.20.0"
-tower = "0.4"
-nix = "0.22.0"
-uuid = "1.4.1"
-axum = "0.6.20"
-tokio = "1.30.0"
-tracing = "0.1.37"
-chrono = "0.4.26"
+subtle = "2.6.1"
+regex = "1.11.1"
+mongodb = "3.1.1"
+once_cell = "1.20.2"
+tower = "0.5"
+nix = "0.29.0"
+uuid = "1.11.0"
+axum = "0.7.9"
+tokio = "1.42.0"
+tracing = "0.1.41"
+chrono = "0.4.39"
+paste = "1.0"
 didcomm = "0.4.1"
-hyper = "0.14.27"
-lazy_static = "1.4.0"
-async-trait = "0.1.73"
-dotenv-flow = "0.15.0"
+hyper = "1.5.2"
+hyper-util = "0.1"
+http-body-util = "0.1"
+lazy_static = "1.5.0"
+async-trait = "0.1.83"
+dotenv-flow = "0.16.2"
 serde_json = "1.0"
-parking_lot = "0.12.0"
-curve25519-dalek = "4.0.0-rc.3"
-ed25519-dalek = "2.0.0-rc.3"
-tracing-subscriber = "0.3.17"
-tower-http = "0.4.3"
+parking_lot = "0.12.3"
+curve25519-dalek = "4.1.3"
+ed25519-dalek = "2.1.1"
+tracing-subscriber = "0.3.19"
+tower-http = "0.6.2"
 base64ct = { version = "1.6.0", default-features = false }
-zeroize = { version = "1.6.0", default-features = false }
+zeroize = { version = "1.8.1", default-features = false }
 
 
 [dependencies]
@@ -104,6 +107,7 @@ tracing.workspace = true
 lazy_static.workspace = true
 serde_json.workspace = true
 hyper.workspace = true
+http-body-util.workspace = true
 tokio = { workspace = true, features = ["full"] }
 tracing-subscriber = { workspace = true, features = ["json"] }
 tower-http = { workspace = true, features = ["catch-panic", "trace", "cors"] }
@@ -135,4 +139,4 @@ mediator-coordination = ["plugin-didcomm_messaging", "didcomm-messaging/mediator
 
 
 [dev-dependencies]
-tower = { version = "0.4.13", features = ["util"] }
+tower = { version = "0.5.2", features = ["util"] }

crates/database/src/lib.rs

@@ -77,7 +77,7 @@ where
         let collection = self.get_collection();
 
         // Lock the Mutex and get the Collection
-        let mut cursor = collection.read().await.find(None, None).await?;
+        let mut cursor = collection.read().await.find(doc! {}).await?;
         while cursor.advance().await? {
             entities.push(cursor.deserialize_current()?);
         }
@@ -91,7 +91,7 @@ where
         // Lock the Mutex and get the Collection
         let collection = collection.read().await;
         Ok(collection
-            .count_documents(filter, None)
+            .count_documents(filter)
             .await?
             .try_into()
             .map_err(|_| RepositoryError::Generic("count overflow".to_owned()))?)
@@ -108,7 +108,7 @@ where
 
         // Lock the Mutex and get the Collection
         let collection = collection.read().await;
-        Ok(collection.find_one(filter, None).await?)
+        Ok(collection.find_one(filter).await?)
     }
 
     /// Stores a new entity.
@@ -119,7 +119,7 @@ where
         let collection = collection.read().await;
 
         // Insert the new entity into the database
-        let metadata = collection.insert_one(entity.clone(), None).await?;
+        let metadata = collection.insert_one(entity.clone()).await?;
 
         // Set the ID if it was inserted and return the updated entity
         if let Bson::ObjectId(oid) = metadata.inserted_id {
@@ -144,7 +144,7 @@ where
         let collection = collection.read().await;
 
         // Retrieve all entities from the database
-        let mut cursor = collection.find(filter, find_options).await?;
+        let mut cursor = collection.find(filter).with_options(find_options).await?;
         while cursor.advance().await? {
             entities.push(cursor.deserialize_current()?);
         }
@@ -160,7 +160,7 @@ where
         let collection = collection.read().await;
 
         // Delete the entity from the database
-        collection.delete_one(doc! {"_id": id}, None).await?;
+        collection.delete_one(doc! {"_id": id}).await?;
 
         Ok(())
     }
@@ -179,8 +179,7 @@ where
         let metadata = collection
             .update_one(
                 doc! {"_id": entity.id().unwrap()},
-                doc! {"$set": bson::to_document(&entity).map_err(|_| RepositoryError::BsonConversionError)?},
-                None,
+                doc! {"$set": bson::to_document(&entity).map_err(|_| RepositoryError::BsonConversionError)?}
             )
             .await?;
 

crates/filesystem/Cargo.toml

@@ -4,7 +4,7 @@ version = "0.1.0"
 edition = "2021"
 
 [dependencies]
-nix.workspace = true
+nix ={ workspace = true, features = ["fs"] }
 
 [features]
 test-utils = []

crates/filesystem/src/lib.rs

@@ -1,14 +1,13 @@
-use nix::fcntl::{flock, FlockArg};
+use nix::fcntl::{Flock, FlockArg};
 use std::{
     fs::OpenOptions,
     io::{Error as IoError, ErrorKind, Result as IoResult},
-    os::unix::io::AsRawFd,
     path::Path,
 };
 
 #[doc(hidden)]
 // Define a trait for file system operations
-pub trait FileSystem: Send + Sync + 'static {
+pub trait FileSystem: Send + 'static {
     fn read_to_string(&self, path: &Path) -> IoResult<String>;
     fn write(&mut self, path: &Path, content: &str) -> IoResult<()>;
     fn read_dir_files(&self, path: &Path) -> IoResult<Vec<String>>;
@@ -54,22 +53,23 @@ impl FileSystem for StdFileSystem {
         let file = OpenOptions::new()
             .read(true)
             .write(true)
+            .truncate(true)
             .create(true)
-            .open(&path)?;
+            .open(path)?;
 
         // Acquire an exclusive lock before writing to the file
-        flock(file.as_raw_fd(), FlockArg::LockExclusive)
+        let file = Flock::lock(file, FlockArg::LockExclusive)
             .map_err(|_| IoError::new(ErrorKind::Other, "Error acquiring file lock"))?;
 
-        std::fs::write(path, &content).map_err(|_| {
+        std::fs::write(path, content).map_err(|_| {
             IoError::new(
                 ErrorKind::Other,
                 "Error saving base64-encoded image to file",
             )
         })?;
 
         // Release the lock after writing to the file
-        flock(file.as_raw_fd(), FlockArg::Unlock)
+        file.unlock()
             .map_err(|_| IoError::new(ErrorKind::Other, "Error releasing file lock"))?;
 
         Ok(())

crates/keystore/src/lib.rs

@@ -42,6 +42,12 @@ where
     collection: Collection<T>,
 }
 
+impl Default for KeyStore<Secrets> {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
 impl KeyStore<Secrets> {
     /// Create a new keystore with default Secrets type.
     ///
@@ -54,10 +60,7 @@ impl KeyStore<Secrets> {
                     let db_lock = db.write().await;
                     db_lock.collection::<Secrets>("secrets").clone()
                 };
-                let collection = tokio::task::block_in_place(|| {
-                    tokio::runtime::Handle::current().block_on(task)
-                });
-                collection
+                tokio::task::block_in_place(|| tokio::runtime::Handle::current().block_on(task))
             })
             .clone();
 

crates/web-plugins/did-endpoint/Cargo.toml

@@ -18,15 +18,16 @@ serde_json.workspace = true
 dotenv-flow.workspace = true
 multibase.workspace = true
 tracing.workspace = true
+http-body-util.workspace = true
 uuid = { workspace = true, features = ["v4"] }
 hyper = { workspace = true, features = ["full"] }
 tokio = { workspace = true, features = ["full"] }
 axum = { workspace = true, features = ["macros"] }
 
 [dev-dependencies]
 async-trait.workspace = true
-mockall = "0.13.0"
+mockall = "0.13.1"
 json-canon = "0.1.3"
 filesystem = { workspace = true, features = ["test-utils"] }
 keystore = { workspace = true, features = ["test-utils"] }
-tower = { version = "0.4.13", features = ["util"] }
+tower = { version = "0.5.2", features = ["util"] }

crates/web-plugins/did-endpoint/src/didgen.rs

@@ -154,7 +154,7 @@ where
 
     // Create directory and write the DID document
     filesystem
-        .create_dir_all(&storage_dirpath)
+        .create_dir_all(storage_dirpath)
         .map_err(|_| Error::PersistenceError)?;
     filesystem
         .write(&storage_dirpath.join("did.json"), &pretty_diddoc)

crates/web-plugins/did-endpoint/src/web.rs

@@ -36,7 +36,7 @@ async fn diddoc(State(state): State<Arc<DidEndPointState>>) -> Result<Json<Value
     let did_path = Path::new(&storage_dirpath).join("did.json");
 
     match filesystem.read_to_string(&did_path).as_ref() {
-        Ok(content) => Ok(Json(serde_json::from_str(&content).map_err(|_| {
+        Ok(content) => Ok(Json(serde_json::from_str(content).map_err(|_| {
             tracing::error!("Unparseable did.json");
             StatusCode::NOT_FOUND
         })?)),
@@ -56,7 +56,7 @@ async fn didpop(
     let diddoc: Document = serde_json::from_value(diddoc_value.clone()).unwrap();
 
     let did_address = diddoc.id.clone();
-    let methods = diddoc.verification_method.clone().unwrap_or(vec![]);
+    let methods = diddoc.verification_method.clone().unwrap_or_default();
 
     // Build verifiable credential (VC)
     let vc: VerifiableCredential = serde_json::from_value(json!({
@@ -157,15 +157,15 @@ async fn didpop(
 fn inspect_vm_relationship(diddoc: &Document, vm_id: &str) -> Option<String> {
     let vrel = [
         (
-            json!(diddoc.authentication.clone().unwrap_or(vec![])),
+            json!(diddoc.authentication.clone().unwrap_or_default()),
             String::from("authentication"),
         ),
         (
-            json!(diddoc.assertion_method.clone().unwrap_or(vec![])),
+            json!(diddoc.assertion_method.clone().unwrap_or_default()),
             String::from("assertionMethod"),
         ),
         (
-            json!(diddoc.key_agreement.clone().unwrap_or(vec![])),
+            json!(diddoc.key_agreement.clone().unwrap_or_default()),
             String::from("keyAgreement"),
         ),
     ];
@@ -199,6 +199,7 @@ mod tests {
         proof::{CryptoProof, EdDsaJcs2022},
         vc::VerifiablePresentation,
     };
+    use http_body_util::BodyExt;
     use serde_json::json;
     use tower::util::ServiceExt;
 
@@ -284,8 +285,8 @@ mod tests {
 
         assert_eq!(response.status(), StatusCode::OK);
 
-        let body = hyper::body::to_bytes(response.into_body()).await.unwrap();
-        let vp: VerifiablePresentation = serde_json::from_slice(&body).unwrap();
+        let body = BodyExt::collect(response.into_body()).await.unwrap();
+        let vp: VerifiablePresentation = serde_json::from_slice(&body.to_bytes()).unwrap();
 
         let vc = vp.verifiable_credential.get(0).unwrap();
         let diddoc = serde_json::from_value(json!(vc.credential_subject)).unwrap();

crates/web-plugins/didcomm-messaging/Cargo.toml

@@ -26,10 +26,10 @@ tracing.workspace = true
 once_cell.workspace = true
 serde_json.workspace = true
 thiserror.workspace = true
+http-body-util.workspace = true
 tokio = { workspace = true, features = ["full"] }
 hyper = { workspace = true, features = ["full"] }
 axum = { workspace = true, features = ["macros"] }
-serde = { version = "1.0", features = ["derive"] }
 
 
 [features]
@@ -50,12 +50,11 @@ mediator-coordination = ["dep:mediator-coordination"]
 
 [dev-dependencies]
 async-trait.workspace = true
-mockall = "0.13.0"
 uuid = { workspace = true, features = ["v4"] }
 json-canon = "0.1.3"
 shared = { workspace = true, features = ["test-utils"] }
-tokio = { version = "1.27.0", default-features = false, features = [
+tokio = { version = "1.42.0", default-features = false, features = [
     "macros",
     "rt",
 ] }
-tower = { version = "0.4.13", features = ["util"] }
+tower = { version = "0.5.2", features = ["util"] }

crates/web-plugins/didcomm-messaging/did-utils/Cargo.toml

@@ -5,11 +5,14 @@ edition = "2021"
 
 [dependencies]
 serde_json.workspace = true
-chrono = { workspace = true, features = ["serde"] }
-hyper = { workspace = true, features = ["client", "http2"] }
 tokio.workspace = true
 serde.workspace = true
+axum.workspace = true
 hyper-tls.workspace = true
+http-body-util.workspace = true
+hyper-util ={ workspace = true, features = ["full"] }
+hyper = { workspace = true, features = ["full"] }
+chrono = { workspace = true, features = ["serde"] }
 
 # Cross-platform random number generator from os
 getrandom = { workspace = true, features = ["js"] }
@@ -38,10 +41,10 @@ subtle.workspace = true
 regex.workspace = true
 
 [dev-dependencies]
-hyper = { version = "0.14.26", features = ["server"] }
-async-std = { version = "1.12.0", features = ["attributes"] }
+hyper = { version = "1.5.2", features = ["server"] }
+async-std = { version = "1.13.0", features = ["attributes"] }
 hex = "0.4.3"
-tokio = { version = "1.27.0", default-features = false, features = [
+tokio = { version = "1.42.0", default-features = false, features = [
     "macros",
     "rt",
 ] }