From 1605df1585defd3e045cb4e727084367a47b0a0e Mon Sep 17 00:00:00 2001
From: janskiba <jan.skiba@dkfz-heidelberg.de>
Date: Thu, 4 Apr 2024 15:27:21 +0200
Subject: [PATCH 1/2] Retry getting catalogue from prism

---
 src/catalogue.rs | 46 ++++++++++++++++++++++++++++++++--------------
 src/main.rs      | 10 +++++++---
 2 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/src/catalogue.rs b/src/catalogue.rs
index d618fa5..888eb9b 100644
--- a/src/catalogue.rs
+++ b/src/catalogue.rs
@@ -1,8 +1,9 @@
-use std::{collections::BTreeMap, time::Duration};
+use std::{collections::BTreeMap, sync::Arc, time::Duration};
 
 use reqwest::Url;
 use serde_json::{json, Value};
-use tracing::{debug, info};
+use tokio::sync::Mutex;
+use tracing::{debug, info, warn};
 
 pub type Criteria = BTreeMap<String, u64>;
 
@@ -16,21 +17,40 @@ fn get_element<'a>(count: &'a CriteriaGroups, key1: &'a str, key2: &'a str, key3
         .and_then(|criteria| criteria.get(key3))
 }
 
+pub fn spawn_thing(catalogue_url: Url, prism_url: Url) -> Arc<Mutex<Value>> {
+    let thing: Arc<Mutex<Value>> = Arc::default();
+    let thing1 = thing.clone();
+    tokio::spawn(async move {
+        tokio::time::sleep(Duration::from_secs(10)).await;    
+        loop {
+            match get_extended_json(catalogue_url.clone(), prism_url.clone()).await {
+                Ok(new_value) => {
+                    *thing1.lock().await = new_value;
+                    info!("Updated Catalogue!");
+                    tokio::time::sleep(Duration::from_secs(60 * 60)).await;
+                },
+                Err(err) => {
+                    warn!("Failed to get thing: {err}.\n Retrying in 5s.");
+                    tokio::time::sleep(Duration::from_secs(5)).await;
+                },
+            }
+        }
+    });
+
+    thing
+}
 
-pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Value {
+pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Result<Value, reqwest::Error> {
     debug!("Fetching catalogue from {catalogue_url} ...");
 
     let resp = reqwest::Client::new()
         .get(catalogue_url)
         .timeout(Duration::from_secs(30))
         .send()
-        .await
-        .expect("Unable to fetch catalogue from upstream; please check URL specified in config.");
+        .await?;
 
-    let mut json: Value = resp.json().await
-        .expect("Unable to parse catalogue from upstream; please check URL specified in config.");
+    let mut json: Value = resp.json().await?;
 
-//    tokio::time::sleep(Duration::from_secs(10)).await;    
 
     let prism_resp = reqwest::Client::new()
         .post(format!("{}criteria", prism_url))
@@ -38,17 +58,15 @@ pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Value {
         .body("{\"sites\": []}")
         .timeout(Duration::from_secs(300))
         .send()
-        .await
-        .expect("Unable to fetch response from Prism; please check it's running.");
+        .await?;
 
-    let mut counts: CriteriaGroups = prism_resp.json().await
-        .expect("Unable to parse response from Prism into CriteriaGroups");
+    let mut counts: CriteriaGroups = prism_resp.json().await?;
 
     recurse(&mut json, &mut counts); //TODO remove from counts once copied into catalogue to make it O(n log n)
 
     info!("Catalogue built successfully.");
 
-    json
+    Ok(json)
 }
 
 /// Key order: group key (e.g. patient)
@@ -119,4 +137,4 @@ fn recurse(json: &mut Value, counts: &mut CriteriaGroups) {
         },
         _ => {}
     }
-}
\ No newline at end of file
+}
diff --git a/src/main.rs b/src/main.rs
index ace0b20..1815d78 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,3 +1,5 @@
+use std::sync::Arc;
+
 use axum::{
     extract::{Json, Path, Query, State},
     http::HeaderValue,
@@ -13,6 +15,7 @@ use once_cell::sync::Lazy;
 use reqwest::{header, Method, StatusCode};
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
+use tokio::sync::Mutex;
 use tower_http::cors::CorsLayer;
 use tracing::{info, warn, Level};
 use tracing_subscriber::{util::SubscriberInitExt, EnvFilter};
@@ -34,7 +37,7 @@ static BEAM_CLIENT: Lazy<BeamClient> = Lazy::new(|| {
 
 #[derive(Clone)]
 struct SharedState {
-    extended_json: Value,
+    extended_json: Arc<Mutex<Value>>,
 }
 
 #[tokio::main]
@@ -53,7 +56,7 @@ async fn main() {
         .allow_headers([header::CONTENT_TYPE]);
 
     let make_service = if let Some(url) = CONFIG.catalogue_url.clone() {
-        let extended_json = catalogue::get_extended_json(url, CONFIG.prism_url.clone()).await;
+        let extended_json = catalogue::spawn_thing(url, CONFIG.prism_url.clone());
         let state = SharedState { extended_json };
 
         let app = Router::new()
@@ -161,5 +164,6 @@ fn convert_response(response: reqwest::Response) -> axum::response::Response {
 }
 
 async fn handle_get_catalogue(State(state): State<SharedState>) -> Json<Value> {
-    Json(state.extended_json)
+    // TODO: We can totally avoid this clone by using axum_extra ErasedJson
+    Json(state.extended_json.lock().await.clone())
 }

From 870c2a16900c15d4b6cc0198c0fc00d7677c9085 Mon Sep 17 00:00:00 2001
From: lablans <m.lablans@dkfz-heidelberg.de>
Date: Thu, 4 Apr 2024 13:36:09 +0000
Subject: [PATCH 2/2] Fix clap choking on empty URL

---
 src/main.rs | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/main.rs b/src/main.rs
index 1815d78..c97c69a 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -48,6 +48,13 @@ async fn main() {
         .finish()
         .init();
 
+    // TODO: Remove this workaround once clap manages to not choke on URL "".
+    if let Ok(var) = std::env::var("CATALOGUE_URL") {
+        if var.is_empty() {
+            std::env::remove_var("CATALOGUE_URL");
+        }
+    }
+
     info!("{:#?}", Lazy::force(&CONFIG));
 
     let cors = CorsLayer::new()