Improve code documentation for the project

crates/database/README.md

@@ -0,0 +1,64 @@
+# Database crate
+
+A lightweight library for managing MongoDB operations. This library provides an interface, the `Repository` trait with default implementations for interacting with MongoDB collections. It is used by the plugins in the workspace that require database access.
+This crate is part of the [DIDComm mediator](https://github.com/adorsys/didcomm-mediator-rs) project.
+
+## Usage
+
+### Requirements
+
+* [MongoDB](https://www.mongodb.com) server instance
+* Environment variables:
+  * `MONGO_URI`: MongoDB connection string
+  * `MONGO_DBN`: Database name
+
+### Example
+
+* Define an entity
+
+```rust
+use database::Repository;
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+struct MyEntity {
+    #[serde(rename = "_id", skip_serializing_if = "Option::is_none")]
+    id: Option<ObjectId>,
+    name: String,
+}
+
+impl Identifiable for MyEntity {
+    fn id(&self) -> Option<ObjectId> {
+        self.id.clone()
+    }
+
+    fn set_id(&mut self, id: ObjectId) {
+        self.id = Some(id);
+    }
+}
+```
+
+* Implement the `Repository` trait(the only required method is `get_collection`)
+
+```rust
+struct MyEntityRepository {
+    collection: Arc<RwLock<Collection<MyEntity>>>,
+}
+
+#[async_trait]
+impl Repository<MyEntity> for MyEntityRepository {
+    fn get_collection(&self) -> Arc<RwLock<Collection<MyEntity>>> {
+        self.collection.clone()
+    }
+}
+```
+
+* Use the repository
+
+```rust
+let db = get_or_init_database();
+let repo = MyEntityRepository {
+    collection: Arc::new(RwLock::new(db.read().await.collection("my_entities"))),
+};
+let entity = MyEntity { id: None, name: "example".to_string() };
+repo.store(entity).await?;
+```

crates/database/src/lib.rs

@@ -68,8 +68,10 @@ where
     Entity: Identifiable + Unpin,
     Entity: Serialize + for<'de> Deserialize<'de>,
 {
+    /// Get a handle to a collection.
     fn get_collection(&self) -> Arc<RwLock<Collection<Entity>>>;
 
+    /// Retrieve all entities from the database.
     async fn find_all(&self) -> Result<Vec<Entity>, RepositoryError> {
         let mut entities = Vec::new();
         let collection = self.get_collection();
@@ -83,7 +85,7 @@ where
         Ok(entities)
     }
 
-    /// Counts all entities by filter.
+    /// Gets the number of documents matching `filter`.
     async fn count_by(&self, filter: BsonDocument) -> Result<usize, RepositoryError> {
         let collection = self.get_collection();
         // Lock the Mutex and get the Collection
@@ -95,10 +97,12 @@ where
             .map_err(|_| RepositoryError::Generic("count overflow".to_owned()))?)
     }
 
+    /// Find an entity by `id`.
     async fn find_one(&self, id: ObjectId) -> Result<Option<Entity>, RepositoryError> {
         self.find_one_by(doc! {"_id": id}).await
     }
 
+    /// Find an entity matching `filter`.
     async fn find_one_by(&self, filter: BsonDocument) -> Result<Option<Entity>, RepositoryError> {
         let collection = self.get_collection();
 
@@ -125,6 +129,8 @@ where
         Ok(entity)
     }
 
+    /// Find all entities matching `filter`.
+    /// If `limit` is set, only the first `limit` entities are returned.
     async fn find_all_by(
         &self,
         filter: BsonDocument,
@@ -146,6 +152,7 @@ where
         Ok(entities)
     }
 
+    /// Deletes an entity by `id`.
     async fn delete_one(&self, id: ObjectId) -> Result<(), RepositoryError> {
         let collection = self.get_collection();
 
@@ -158,6 +165,7 @@ where
         Ok(())
     }
 
+    /// Updates an entity.
     async fn update(&self, entity: Entity) -> Result<Entity, RepositoryError> {
         if entity.id().is_none() {
             return Err(RepositoryError::MissingIdentifier);

crates/keystore/README.md

@@ -0,0 +1,40 @@
+# Keystore Crate
+
+The `keystore` crate is a utility library for managing cryptographic secrets. It is used in the [Didcomm Mediator](https://github.com/adorsys/didcomm-mediator-rs/) to store and retrieve cryptographic keys for DIDcomm interactions.
+
+## Usage
+
+This crate is internal to the [Didcomm Mediator](https://github.com/adorsys/didcomm-mediator-rs/). Below is an example of interacting with the keystore:
+
+```rust
+use keystore::{KeyStore, Secrets};
+use mongodb::bson::{doc, Bson, Document};
+use did_utils::jwk::Jwk;
+
+// Initialize the keystore
+let keystore = KeyStore::get();
+
+let jwk: Jwk = serde_json::from_str(
+    r#"{
+        "kty": "OKP",
+        "crv": "X25519",
+        "x": "SHSUZ6V3x355FqCzIUfgoPzrZB0BQs0JKyag4UfMqHQ",
+        "d": "0A8SSFkGHg3N9gmVDRnl63ih5fcwtEvnQu9912SVplY"
+    }"#,
+)
+.unwrap();
+
+// Store a secret
+let secret = Secrets {
+    id: Some(ObjectId::new()),
+    kid: "key-1".to_string(),
+    secret_material: jwk,
+};
+keystore.store(secret).await?;
+
+// Retrieve a secret by ID
+let secret = keystore.find_one(doc! {"kid": "key-1"}).await?;
+
+// Delete a secret by ID
+keystore.delete_one(secret.id.unwrap()).await?;
+```

crates/keystore/src/lib.rs

@@ -9,6 +9,7 @@ use tokio::sync::RwLock;
 
 static SECRETS_COLLECTION: OnceCell<Collection<Secrets>> = OnceCell::new();
 
+/// Represents a cryptographic secret stored in the keystore.
 #[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
 pub struct Secrets {
     #[serde(rename = "_id")]
@@ -30,6 +31,7 @@ impl Identifiable for Secrets {
     }
 }
 
+/// A keystore for managing cryptographic secrets.
 #[derive(Debug, Clone)]
 pub struct KeyStore<T>
 where

crates/plugin-api/README.md

@@ -1,6 +1,6 @@
 # Server plugin API
 
-The server used for this project provides a system for building versatile applications by integrating functionalities offered by configurable plugins via the plugin API.
+An interface that can be used by a generic server to build versatile applications by integrating functionalities offered by configurable plugins via the plugin API. It is part of the [Didcomm Mediator](https://github.com/adorsys/didcomm-mediator-rs/) project.
 
 ## Features
 
@@ -51,9 +51,9 @@ impl Plugin for MyPlugin {
         Ok(())
     }
 
-    fn routes(&self) -> Router {
+    fn routes(&self) -> Result<Router, PluginError> {
         // Define and return routes here
-        Router::new().route("/myplugin", get(my_plugin_handler))
+        Router::new().route("/myplugin", get(my_plugin_handler))?
     }
 }
 

crates/web-plugins/did-endpoint/README.md

@@ -1,32 +1,35 @@
 # did-endpoint
 
-The `did-endpoint` crate provides tools and functionalities for generating and managing Decentralized Identifiers (DIDs) and web-based interactions.
+The `did-endpoint` plugin crate provides a set of tools for generating and validating a DID document. It is a part of the [Didcomm Mediator](https://github.com/adorsys/didcomm-mediator-rs/) project.
 
 ## Features
 
-- **Generates keys and forward them for DID generation:**
 - **Builds and persists DID document:**
 - **Validates the integrity of the persisted DID document**
 
-## Usage
-
-To use `did-endpoint` in your project, add the following to your **Cargo.toml**:
-
-```toml
-did-endpoint = "0.1.0"
-```
-
 ### Example
 
 Here’s a simple example of how you can generate and validate a DID document:
 
 ```rust
 use did_endpoint::{didgen, validate_diddoc};
+use filesystem::{FileSystem, StdFileSystem};
+use keystore::KeyStore;
+
+let storage_dirpath = std::env::var("STORAGE_DIRPATH").unwrap(),
+let server_public_domain = std::env::var("SERVER_PUBLIC_DOMAIN").unwrap();
+
+let mut filesystem = filesystem::StdFileSystem;
+let keystore = keystore::KeyStore::get();
 
-let (storage_dirpath, server_public_domain) = ("target/storage", "https://example.com");
+// Generate and persist a new DID document
+didgen::didgen(
+    storage_dirpath,
+    server_public_domain,
+    &keystore,
+    &mut filesystem,
+)?;
 
-// generate and persist a did document
-didgen(&storage_dirpath, &server_public_domain)?;
-// validate the generated did document
-assert!(validate_diddoc(&storage_dirpath).is_ok());
+// Validate the integrity of the persisted DID document
+didgen::validate_diddoc(storage_dirpath, &keystore, &mut filesystem)?;
 ```

crates/web-plugins/didcomm-messaging/README.md

@@ -0,0 +1,97 @@
+# didcomm-messaging
+
+The `didcomm-messaging` plugin is a web plugin of the [DIDComm mediator](https://github.com/adorsys/didcomm-mediator-rs/) project. It provides implementations of various DIDComm messaging protocols as plugins and features, so protocols can be added and deleted with minimal effort as well as being dynamically loaded.
+
+See the repository [README](https://github.com/adorsys/didcomm-mediator-rs/blob/main/README.md) for the list of currently supported protocols.
+
+## Usage
+
+**Implementing a new protocol:**
+
+* Define handler(s) for the protocol
+
+```rust
+use async_trait::async_trait;
+use axum::response::{IntoResponse, Response};
+use didcomm::Message;
+use message_api::{MessageHandler, MessagePlugin, MessageRouter};
+use shared::state::AppState;
+use std::sync::Arc;
+
+pub struct MockProtocol;
+
+struct ExampleProtocolHandler1;
+struct ExampleProtocolHandler2;
+
+#[async_trait]
+impl MessageHandler for ExampleProtocolHandler1 {
+    async fn handle(
+        &self,
+        _state: Arc<AppState>,
+        message: Message,
+    ) -> Result<Option<Message>, Response> {
+        // do something with the message
+        Ok(None)
+    }
+}
+
+#[async_trait]
+impl MessageHandler for ExampleProtocolHandler2 {
+    async fn handle(
+        &self,
+        _state: Arc<AppState>,
+        message: Message,
+    ) -> Result<Option<Message>, Response> {
+        // do something with the message
+        Ok(None)
+    }
+}
+
+impl MessagePlugin for MockProtocol {
+    fn name(&self) -> &'static str {
+        "mock_protocol"
+    }
+
+    fn didcomm_routes(&self) -> MessageRouter {
+        MessageRouter::new()
+            .register("message-type-1", ExampleProtocolHandler1)
+            .register("message-type-2", ExampleProtocolHandler2)
+    }
+}
+```
+
+* Add the protocol to the `DIDCOMM_PLUGINS` array in `crates/web-plugins/didcomm-messaging/src/protocols.rs`:
+
+```rust
+pub(crate) static DIDCOMM_PLUGINS: Lazy<Vec<Arc<dyn MessagePlugin>>> = Lazy::new(|| {
+    vec![
+        #[cfg(feature = "mock-protocol")]
+        Arc::new(MockProtocol),
+        // other plugins
+    ]
+});
+```
+
+* Add the plugin as a feature in `didcomm-messaging` `Cargo.toml`:
+
+```toml
+[dependencies]
+mock-protocol = { workspace = true, optional = true }
+
+[features]
+mock-protocol = ["mock-protocol", ...]
+
+default = ["mock-protocol", ...]
+```
+
+* Adjust the workspace `Cargo.toml`:
+
+```toml
+[workspace.dependencies]
+mock-protocol = { path = "./crates/web-plugins/didcomm-messaging/protocols/mock-protocol", version = "0.1.0" }
+
+[features]
+mock-protocol = ["plugin-didcomm_messaging", "didcomm-messaging/mock-protocol"]
+```
+
+The plugin manager will automatically handle routing based on the added protocol's routes.

crates/web-plugins/didcomm-messaging/did-utils/README.md

@@ -10,8 +10,11 @@ A Rust library for implementing reusable utility code for DID-based applications
 
 ## Installation
 
-```rust
-cargo install did-utils
+Add this to your `Cargo.toml`:
+
+```toml
+[dependencies]
+did-utils = "0.1"
 ```
 
 ## Usage
@@ -39,20 +42,9 @@ let encrypted_did_document = did_document.encrypt(&my_public_key);
 let decrypted_did_document = encrypted_did_document.decrypt(&my_private_key);
 ```
 
-## Dependencies
-
-* serde
-* sha2
-* x25519-dalek
-
 ## Documentation
 
-The documentation for the library is available here: https://docs.rs/did-utils/
-
-## Contributors
-
-* Bard
-* [Your name]
+The documentation for the library is available [here](https://docs.rs/did-utils)
 
 ## License