Merge pull request #290 from umccr/fix/deny-unknown-fields

feat: deny unknown fields in config

htsget-config/src/config/advanced/allow_guard.rs

@@ -14,7 +14,7 @@ pub trait QueryAllowed {
 
 /// A query guard represents query parameters that can be allowed to storage for a given query.
 #[derive(Serialize, Clone, Debug, Deserialize, PartialEq, Eq)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct AllowGuard {
   allow_reference_names: ReferenceNames,
   allow_fields: Fields,
@@ -39,7 +39,7 @@ impl Default for AllowGuard {
 
 /// Reference names that can be matched.
 #[derive(Clone, Debug, Deserialize, Serialize, PartialEq, Eq)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 pub enum ReferenceNames {
   Tagged(TaggedTypeAll),
   List(HashSet<String>),

htsget-config/src/config/advanced/cors.rs

@@ -18,6 +18,7 @@ const CORS_MAX_AGE: usize = 2592000;
 
 /// Tagged allow headers for cors config, either Mirror or Any.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub enum TaggedAllowTypes {
   #[serde(alias = "mirror", alias = "MIRROR")]
   Mirror,
@@ -27,7 +28,7 @@ pub enum TaggedAllowTypes {
 
 /// Allowed type for cors config which is used to configure cors behaviour.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 pub enum AllowType<T, Tagged = TaggedAllowTypes> {
   Tagged(Tagged),
   #[serde(bound(serialize = "T: Display", deserialize = "T: FromStr, T::Err: Display"))]
@@ -159,7 +160,7 @@ impl Display for HeaderValue {
 
 /// Cors configuration for the htsget server.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct CorsConfig {
   allow_credentials: bool,
   allow_origins: AllowType<HeaderValue>,

htsget-config/src/config/advanced/mod.rs

@@ -11,6 +11,7 @@ pub mod url;
 
 /// Determines which tracing formatting style to use.
 #[derive(Debug, Copy, Clone, Serialize, Deserialize, Default)]
+#[serde(deny_unknown_fields)]
 pub enum FormattingStyle {
   #[default]
   Full,

htsget-config/src/config/advanced/regex_location.rs

@@ -9,7 +9,7 @@ use serde::{Deserialize, Serialize};
 
 /// A regex storage is a storage that matches ids using Regex.
 #[derive(Serialize, Debug, Clone, Deserialize)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct RegexLocation {
   #[serde(with = "serde_regex")]
   regex: Regex,

htsget-config/src/config/advanced/url.rs

@@ -15,6 +15,7 @@ use serde::{Deserialize, Serialize};
 
 /// Options for the remote URL server config.
 #[derive(Serialize, Deserialize, Debug, Clone)]
+#[serde(deny_unknown_fields)]
 pub struct Url {
   #[serde(with = "http_serde::uri")]
   url: Uri,

htsget-config/src/config/data_server.rs

@@ -11,14 +11,15 @@ use std::path::{Path, PathBuf};
 
 /// Tagged allow headers for cors config, either Mirror or Any.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub enum DataServerTagged {
   #[serde(alias = "none", alias = "NONE", alias = "null")]
   None,
 }
 
 /// Whether the data server is enabled or not.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 #[allow(clippy::large_enum_variant)]
 pub enum DataServerEnabled {
   None(DataServerTagged),
@@ -38,7 +39,7 @@ impl DataServerEnabled {
 
 /// Configuration for the htsget server.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct DataServerConfig {
   addr: SocketAddr,
   local_path: PathBuf,

htsget-config/src/config/location.rs

@@ -15,7 +15,7 @@ use {crate::config::advanced::url::Url, crate::error, http::Uri};
 
 /// The locations of data.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(default, from = "LocationsOneOrMany")]
+#[serde(default, deny_unknown_fields, from = "LocationsOneOrMany")]
 pub struct Locations(Vec<LocationEither>);
 
 impl Locations {
@@ -48,7 +48,7 @@ impl Default for Locations {
 
 /// Either simple or regex based location
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 pub enum LocationEither {
   Simple(Location),
   Regex(RegexLocation),

htsget-config/src/config/mod.rs

@@ -50,7 +50,7 @@ struct Args {
 
 /// Simplified config.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct Config {
   ticket_server: TicketServerConfig,
   data_server: DataServerEnabled,

htsget-config/src/config/service_info.rs

@@ -8,7 +8,7 @@ use std::collections::HashMap;
 
 /// Service info config.
 #[derive(Serialize, Debug, Clone, Default, PartialEq, Eq)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct ServiceInfo(HashMap<String, Value>);
 
 impl ServiceInfo {

htsget-config/src/config/ticket_server.rs

@@ -8,7 +8,7 @@ use std::net::SocketAddr;
 
 /// Configuration for the htsget ticket server.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct TicketServerConfig {
   addr: SocketAddr,
   #[serde(skip_serializing)]

htsget-config/src/storage/c4gh/local.rs

@@ -9,6 +9,7 @@ use std::path::PathBuf;
 
 /// Local C4GH key storage.
 #[derive(Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub struct C4GHLocal {
   private: PathBuf,
   public: PathBuf,

htsget-config/src/storage/c4gh/mod.rs

@@ -19,7 +19,7 @@ pub mod secrets_manager;
 
 /// Config for Crypt4GH keys.
 #[derive(Deserialize, Debug, Clone)]
-#[serde(try_from = "C4GHKeyLocation")]
+#[serde(try_from = "C4GHKeyLocation", deny_unknown_fields)]
 pub struct C4GHKeys {
   // Store a cloneable future so that it can be resolved outside serde.
   keys: Shared<BoxFuture<'static, Result<Vec<crypt4gh::Keys>>>>,
@@ -74,7 +74,7 @@ impl TryFrom<C4GHKeyLocation> for C4GHKeys {
 
 /// The location of C4GH keys.
 #[derive(Deserialize, Debug, Clone)]
-#[serde(tag = "kind")]
+#[serde(tag = "kind", deny_unknown_fields)]
 #[non_exhaustive]
 pub enum C4GHKeyLocation {
   #[serde(alias = "file", alias = "FILE")]

htsget-config/src/storage/c4gh/secrets_manager.rs

@@ -16,6 +16,7 @@ use tempfile::TempDir;
 
 /// C4GH secrets manager key storage.
 #[derive(Deserialize, Debug, Clone)]
+#[serde(deny_unknown_fields)]
 pub struct C4GHSecretsManager {
   private: String,
   public: String,

htsget-config/src/storage/file.rs

@@ -15,7 +15,7 @@ use std::str::FromStr;
 
 /// Local file based storage.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct File {
   scheme: Scheme,
   #[serde(with = "http_serde::authority")]

htsget-config/src/storage/mod.rs

@@ -37,7 +37,7 @@ impl ResolvedId {
 
 /// Specify the storage backend to use as config values.
 #[derive(Serialize, Deserialize, Debug, Clone)]
-#[serde(tag = "kind")]
+#[serde(tag = "kind", deny_unknown_fields)]
 #[non_exhaustive]
 pub enum Backend {
   #[serde(alias = "file", alias = "FILE")]

htsget-config/src/storage/s3.rs

@@ -7,7 +7,7 @@ use serde::{Deserialize, Serialize};
 
 /// Configuration struct for S3 storage.
 #[derive(Serialize, Deserialize, Debug, Clone, Default)]
-#[serde(default)]
+#[serde(default, deny_unknown_fields)]
 pub struct S3 {
   bucket: String,
   endpoint: Option<String>,

htsget-config/src/storage/url.rs

@@ -10,7 +10,7 @@ use serde::{Deserialize, Serialize};
 
 /// Remote URL server storage struct.
 #[derive(Deserialize, Serialize, Debug, Clone)]
-#[serde(try_from = "advanced::url::Url")]
+#[serde(try_from = "advanced::url::Url", deny_unknown_fields)]
 pub struct Url {
   #[serde(with = "http_serde::uri")]
   url: Uri,

htsget-config/src/tls/client.rs

@@ -11,7 +11,7 @@ use serde::Deserialize;
 /// A certificate and key pair used for TLS. Serialization is not implemented because there
 /// is no way to convert back to a `PathBuf`.
 #[derive(Deserialize, Debug, Clone, Default)]
-#[serde(try_from = "RootCertStorePair")]
+#[serde(try_from = "RootCertStorePair", deny_unknown_fields)]
 pub struct TlsClientConfig {
   cert: Option<Vec<Certificate>>,
   identity: Option<Identity>,

htsget-config/src/tls/mod.rs

@@ -29,7 +29,7 @@ pub trait KeyPairScheme {
 /// A certificate and key pair used for TLS. Serialization is not implemented because there
 /// is no way to convert back to a `PathBuf`.
 #[derive(Deserialize, Debug, Clone)]
-#[serde(try_from = "CertificateKeyPairPath")]
+#[serde(try_from = "CertificateKeyPairPath", deny_unknown_fields)]
 pub struct TlsServerConfig {
   server_config: ServerConfig,
 }
@@ -49,6 +49,7 @@ impl TlsServerConfig {
 /// The location of a certificate and key pair used for TLS.
 /// This is the path to the PEM formatted X.509 certificate and private key.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub struct CertificateKeyPairPath {
   cert: PathBuf,
   key: PathBuf,
@@ -76,6 +77,7 @@ impl CertificateKeyPair {
 /// The location of a certificate and key pair used for TLS.
 /// This is the path to the PEM formatted X.509 certificate and private key.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub struct RootCertStorePair {
   #[serde(flatten)]
   key_pair: Option<CertificateKeyPairPath>,

htsget-config/src/types.rs

@@ -21,7 +21,7 @@ pub type Result<T> = result::Result<T, HtsGetError>;
 
 /// An enumeration with all the possible formats.
 #[derive(Copy, Clone, Debug, PartialEq, Eq, Serialize, Deserialize)]
-#[serde(rename_all(serialize = "UPPERCASE"))]
+#[serde(rename_all(serialize = "UPPERCASE"), deny_unknown_fields)]
 pub enum Format {
   #[serde(alias = "bam", alias = "BAM")]
   Bam,
@@ -112,7 +112,7 @@ impl Display for Format {
 
 /// Class component of htsget response.
 #[derive(Copy, Debug, PartialEq, Eq, Clone, Serialize, Deserialize)]
-#[serde(rename_all(serialize = "lowercase"))]
+#[serde(rename_all(serialize = "lowercase"), deny_unknown_fields)]
 pub enum Class {
   #[serde(alias = "header", alias = "HEADER")]
   Header,
@@ -123,6 +123,7 @@ pub enum Class {
 /// An interval represents the start (0-based, inclusive) and end (0-based exclusive) ranges of the
 /// query.
 #[derive(Copy, Clone, Debug, Default, PartialEq, Eq, Deserialize, Serialize)]
+#[serde(deny_unknown_fields)]
 pub struct Interval {
   start: Option<u32>,
   end: Option<u32>,
@@ -205,7 +206,7 @@ impl Interval {
 
 /// Schemes that can be used with htsget.
 #[derive(Serialize, Deserialize, Debug, Default, Clone, Copy, PartialEq, Eq)]
-#[serde(rename_all = "UPPERCASE")]
+#[serde(rename_all = "UPPERCASE", deny_unknown_fields)]
 pub enum Scheme {
   #[default]
   #[serde(alias = "Http", alias = "http")]
@@ -225,14 +226,15 @@ impl Display for Scheme {
 
 /// Tagged Any allow type for cors config.
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)]
+#[serde(deny_unknown_fields)]
 pub enum TaggedTypeAll {
   #[serde(alias = "all", alias = "ALL")]
   All,
 }
 
 /// Possible values for the fields parameter.
 #[derive(Clone, Debug, PartialEq, Eq, Deserialize, Serialize)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 pub enum Fields {
   /// Include all fields
   Tagged(TaggedTypeAll),
@@ -242,7 +244,7 @@ pub enum Fields {
 
 /// Possible values for the tags parameter.
 #[derive(Clone, Debug, PartialEq, Eq, Deserialize, Serialize)]
-#[serde(untagged)]
+#[serde(untagged, deny_unknown_fields)]
 pub enum Tags {
   /// Include all tags
   Tagged(TaggedTypeAll),
@@ -252,6 +254,7 @@ pub enum Tags {
 
 /// The no tags parameter.
 #[derive(Clone, Debug, PartialEq, Eq, Deserialize, Serialize)]
+#[serde(deny_unknown_fields)]
 pub struct NoTags(pub Option<HashSet<String>>);
 
 /// A struct containing the information from the HTTP request.
@@ -516,6 +519,7 @@ impl From<io::Error> for HtsGetError {
 
 /// The headers that need to be supplied when requesting data from a url.
 #[derive(Debug, Default, PartialEq, Eq, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
 pub struct Headers(HashMap<String, String>);
 
 impl Headers {
@@ -585,6 +589,7 @@ impl TryFrom<&HeaderMap> for Headers {
 
 /// A url from which raw data can be retrieved.
 #[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
 pub struct Url {
   pub url: String,
   #[serde(skip_serializing_if = "Option::is_none")]
@@ -635,6 +640,7 @@ impl Url {
 
 /// Wrapped json response for htsget.
 #[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
 pub struct JsonResponse {
   pub htsget: Response,
 }
@@ -654,6 +660,7 @@ impl From<Response> for JsonResponse {
 
 /// The response for a HtsGet query.
 #[derive(Debug, PartialEq, Eq, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
 pub struct Response {
   pub format: Format,
   pub urls: Vec<Url>,