feat: snake_case in REST APIs and rename /tx/csq to /seqvars/csq (#150)…

… (#189)

.github/workflows/rust.yml

@@ -102,21 +102,22 @@ jobs:
 
       - uses: Swatinem/rust-cache@v2
         with:
+          key: "${{ matrix.label }}"
           cache-directories: |
             ~/.cargo/registry/src/**/librocksdb-sys-*
 
       - name: Run cargo-tarpaulin with fast tests
         uses: actions-rs/[email protected]
         with:
           version: 0.21.0
-          args: "-- --test-threads 1"
+          args: "--skip-clean -- --test-threads 1"
         if: ${{ matrix.label == 'fast' }}
 
       - name: Run cargo-tarpaulin with full tests
         uses: actions-rs/[email protected]
         with:
           version: 0.21.0
-          args: "--release --timeout=180 -- --include-ignored"
+          args: "--skip-clean --release --timeout=180 -- --include-ignored"
         if: ${{ matrix.label == 'full' }}
 
       - name: Codecov submission of fast test results

src/common.rs

@@ -29,7 +29,7 @@ pub fn trace_rss_now() {
 #[derive(
     clap::ValueEnum, serde::Serialize, serde::Deserialize, Clone, Copy, Debug, PartialEq, Eq, Hash,
 )]
-#[serde(rename_all = "kebab-case")]
+#[serde(rename_all = "snake_case")]
 pub enum GenomeRelease {
     Grch37,
     Grch38,
@@ -95,7 +95,7 @@ pub fn version() -> &'static str {
 /// Version information that is returned by the HTTP server.
 #[derive(serde::Serialize, serde::Deserialize, Default, Debug, Clone)]
 #[serde_with::skip_serializing_none]
-#[serde(rename_all = "kebab-case")]
+#[serde(rename_all = "snake_case")]
 pub struct Version {
     /// Version of the transcript database data.
     pub tx_db: Option<String>,

src/server/actix_server/mod.rs

@@ -5,8 +5,8 @@ use actix_web::ResponseError;
 use crate::annotate::strucvars::csq::ConsequencePredictor as StrucvarConsequencePredictor;
 use crate::{annotate::seqvars::csq::ConsequencePredictor, common::GenomeRelease};
 
+pub mod seqvars_csq;
 pub mod strucvars_csq;
-pub mod tx_csq;
 
 #[derive(Debug)]
 struct CustomError {
@@ -47,7 +47,7 @@ pub async fn main(
     actix_web::HttpServer::new(move || {
         actix_web::App::new()
             .app_data(data.clone())
-            .service(tx_csq::handle)
+            .service(seqvars_csq::handle)
             .service(strucvars_csq::handle)
             .wrap(actix_web::middleware::Logger::default())
     })

src/server/actix_server/tx_csq.rs → src/server/actix_server/seqvars_csq.rs

@@ -1,4 +1,4 @@
-//! Implementation of `/tx/csq` endpoint.
+//! Implementation of `/seqvars/csq` endpoint.
 
 use actix_web::{
     get,
@@ -16,10 +16,10 @@ use crate::{
     common::GenomeRelease,
 };
 
-/// Parameters for `/tx/csq`.
+/// Parameters for `/seqvars/csq`.
 ///
 #[derive(serde::Serialize, serde::Deserialize, Debug, Clone)]
-#[serde(rename_all = "kebab-case")]
+#[serde(rename_all = "snake_case")]
 #[serde_with::skip_serializing_none]
 struct Query {
     /// The assembly.
@@ -38,7 +38,7 @@ struct Query {
 
 /// Result entry for the API.
 #[derive(Debug, serde::Serialize, serde::Deserialize)]
-#[serde(rename_all = "kebab-case")]
+#[serde(rename_all = "snake_case")]
 struct ResultEntry {
     /// The consequences of the allele.
     pub consequences: Vec<Consequence>,
@@ -85,7 +85,7 @@ struct Container {
 
 /// Query for consequence of a variant.
 #[allow(clippy::unused_async)]
-#[get("/tx/csq")]
+#[get("/seqvars/csq")]
 async fn handle(
     data: Data<super::WebServerData>,
     _path: Path<()>,

src/server/mod.rs

@@ -50,14 +50,21 @@ pub fn print_hints(args: &Args) {
     // The endpoint `/tx/csq` to comput ethe consequence of a variant; without and with filtering
     // for HGNC gene ID.
     tracing::info!(
-        "  try: http://{}:{}/tx/csq?genome-release=grch37\
+        "  try: http://{}:{}/seqvars/csq?genome_release=grch37\
         &chromosome=17&position=48275363&reference=C&alternative=A",
         args.listen_host.as_str(),
         args.listen_port
     );
     tracing::info!(
-        "  try: http://{}:{}/tx/csq?genome-release=grch37\
-        &chromosome=17&position=48275363&reference=C&alternative=A&hgnc-id=HGNC:2197",
+        "  try: http://{}:{}/seqvars/csq?genome_release=grch37\
+        &chromosome=17&position=48275363&reference=C&alternative=A&hgnc_id=HGNC:2197",
+        args.listen_host.as_str(),
+        args.listen_port
+    );
+    // The endpoint `/strucvars/csq` computes the consequence of an SV.
+    tracing::info!(
+        "  try: http://{}:{}/strucvars/csq?genome_release=grch37\
+        &chromosome=17&start=48275360&&stop=48275370&sv_type=DEL",
         args.listen_host.as_str(),
         args.listen_port
     );