WIP: Added new endpoint /catalogue to return catalogue defined in CAT…

…ALOGUE_URL env var, extended with counts.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "spot"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 license = "Apache-2.0"
 documentation = "https://github.com/samply/spot"
@@ -20,7 +20,7 @@ once_cell = "1"
 # Logging
 tracing = "0.1.37"
 tracing-subscriber = { version = "0.3.17", features = ["env-filter"] }
-reqwest = { version = "0.11.20", default-features = false, features = ["stream"] }
+reqwest = { version = "0.11.20", default-features = false, features = ["stream", "default-tls"] }
 tower-http = { version = "0.4.4", features = ["cors"] }
 
 [build-dependencies]

src/banner.rs

@@ -10,7 +10,7 @@ pub(crate) fn print_banner() {
         _ => "SNAPSHOT",
     };
     info!(
-        "🌈 Samply.Spot v{} (built {} {}, {}) starting up ...",
+        "🌈 Samply.Spot v{} (built {} {}, {}) ready to take requests.",
         env!("CARGO_PKG_VERSION"),
         env!("BUILD_DATE"),
         env!("BUILD_TIME"),

src/catalogue.rs

@@ -0,0 +1,100 @@
+use reqwest::Url;
+use serde::{Deserialize, Serialize};
+use serde_json::{json, Value};
+use tracing::{debug, info};
+
+#[derive(Serialize, Deserialize)]
+#[serde(rename_all = "UPPERCASE")]
+enum ChildCategoryType {
+    Equals,
+    SomethingElse
+}
+
+#[derive(Serialize, Deserialize)]
+struct ChildCategoryCriterion {
+    key: String,
+    count: Option<usize>
+}
+
+#[derive(Serialize, Deserialize)]
+struct ChildCategory {
+    key: String,
+    type_: ChildCategoryType,
+    criteria: Vec<ChildCategoryCriterion>
+}
+
+pub async fn get_extended_json(catalogue_url: Url) -> Value {
+    debug!("Fetching catalogue from {catalogue_url} ...");
+    let resp = reqwest::get(catalogue_url).await
+        .expect("Unable to fetch catalogue from upstream; please check URL specified in config.");
+
+    let mut json: Value = resp.json().await
+        .expect("Unable to parse catalogue from upstream; please check URL specified in config.");
+
+    // TODO: Query prism for counts here.
+
+    recurse(&mut json);
+
+    // println!("{}", serde_json::to_string_pretty(&json).unwrap());
+
+    info!("Catalogue built successfully.");
+
+    json
+}
+
+/// Key order: group key (e.g. patient)
+///            \-- stratifier key (e.g. admin_gender)
+///                \-- stratum key (e.g. male, other)
+fn recurse(json: &mut Value) {
+    match json {
+        Value::Null => (),
+        Value::Bool(_) => (),
+        Value::Number(_) => (),
+        Value::String(_) => (),
+        Value::Array(arr) => {
+            for ele in arr {
+                recurse(ele);
+            }
+        },
+        Value::Object(obj) => {
+            if ! obj.contains_key("childCategories") {
+                for (_key, child_val) in obj.iter_mut() {
+                    recurse(child_val);
+                }
+            } else {
+                let group_key = obj.get("key").expect("Got JSON element with childCategories but without (group) key. Please check json.");
+
+                let children_cats = obj
+                    .get_mut("childCategories")
+                    .unwrap()
+                    .as_array_mut()
+                    .unwrap()
+                    .iter_mut()
+                    .filter(|item| item.get("type").unwrap_or(&Value::Null) == "EQUALS");
+
+                for child_cat in children_cats {
+                    let stratifier_key = child_cat.get("key").expect("Got JSON element with childCategory that does not contain a (stratifier) key. Please check json.");
+                    let criteria = child_cat
+                        .get_mut("criteria")
+                        .expect("Got JSON element with childCategory that does not contain a criteria array. Please check json.")
+                        .as_array_mut()
+                        .expect("Got JSON element with childCategory with criteria that are not an array. Please check json.");
+
+                    for criterion in criteria {
+                        let criterion = criterion.as_object_mut()
+                            .expect("Got JSON where a criterion was not an object. Please check json.");
+                        let stratum_key = criterion.get("key")
+                            .expect("Got JSON where a criterion did not have a key. Please check json.")
+                            .as_str()
+                            .expect("Got JSON where a criterion key was not a string. Please check json.");
+
+                        // fetch from Prism output
+                        let count_from_prism = 10;
+
+                        criterion.insert("count".into(), json!(count_from_prism));
+                    }
+                }
+            }
+        },
+    }
+}

src/config.rs

@@ -31,6 +31,10 @@ pub struct Config {
     /// The socket address this server will bind to
     #[clap(long, env, default_value = "0.0.0.0:8080")]
     pub bind_addr: SocketAddr,
+
+    /// URL to catalogue.json file
+    #[clap(long, env)]
+    pub catalogue_url: Url
 }
 
 fn parse_cors(v: &str) -> Result<AllowOrigin, InvalidHeaderValue> {

src/main.rs

@@ -1,5 +1,5 @@
 use axum::{
-    extract::{Json, Path, Query},
+    extract::{Json, Path, Query, State},
     http::HeaderValue,
     response::{IntoResponse, Response},
     routing::{get, post},
@@ -12,12 +12,14 @@ use config::Config;
 use once_cell::sync::Lazy;
 use reqwest::{header, Method, StatusCode};
 use serde::{Deserialize, Serialize};
+use serde_json::Value;
 use tower_http::cors::CorsLayer;
 use tracing::{info, warn, Level};
 use tracing_subscriber::{EnvFilter, util::SubscriberInitExt};
 
 mod banner;
 mod beam;
+mod catalogue;
 mod config;
 
 static CONFIG: Lazy<Config> = Lazy::new(Config::parse);
@@ -30,6 +32,11 @@ static BEAM_CLIENT: Lazy<BeamClient> = Lazy::new(|| {
     )
 });
 
+#[derive(Clone)]
+struct SharedState {
+    extended_json: Value
+}
+
 #[tokio::main]
 async fn main() {
     tracing_subscriber::FmtSubscriber::builder()
@@ -40,9 +47,9 @@ async fn main() {
 
     info!("{:#?}", Lazy::force(&CONFIG));
 
-
+    let extended_json = catalogue::get_extended_json(CONFIG.catalogue_url.clone()).await;
+    let state = SharedState { extended_json };
 
-    banner::print_banner();
     // TODO: Add check for reachability of beam-proxy
 
     let cors = CorsLayer::new()
@@ -53,9 +60,13 @@ async fn main() {
     let app = Router::new()
         .route("/beam", post(handle_create_beam_task))
         .route("/beam/:task_id", get(handle_listen_to_beam_tasks))
+        .route("/catalogue", get(handle_get_catalogue))
+        .with_state(state)
         .layer(axum::middleware::map_response(banner::set_server_header))
         .layer(cors);
 
+    banner::print_banner();
+
     axum::Server::bind(&CONFIG.bind_addr)
         .serve(app.into_make_service())
         .await
@@ -133,3 +144,9 @@ fn convert_response(response: reqwest::Response) -> axum::response::Response {
         .unwrap()
         .into_response()
 }
+
+async fn handle_get_catalogue(
+    State(state): State<SharedState>
+) -> Json<Value> {
+    Json(state.extended_json)
+}