From 036486c421880756c44b60da98c9f5777ba49383 Mon Sep 17 00:00:00 2001 From: Enola Knezevic Date: Thu, 4 Apr 2024 14:59:13 +0200 Subject: [PATCH 1/3] optional prism --- src/catalogue.rs | 65 ++++++++++++++++++------------------------------ src/config.rs | 2 +- src/main.rs | 39 ++++++++++++++++++----------- 3 files changed, 50 insertions(+), 56 deletions(-) diff --git a/src/catalogue.rs b/src/catalogue.rs index 67ee22d..d618fa5 100644 --- a/src/catalogue.rs +++ b/src/catalogue.rs @@ -1,7 +1,6 @@ use std::{collections::BTreeMap, time::Duration}; use reqwest::Url; -use serde::{Deserialize, Serialize}; use serde_json::{json, Value}; use tracing::{debug, info}; @@ -11,18 +10,13 @@ pub type CriteriaGroup = BTreeMap; pub type CriteriaGroups = BTreeMap; -fn get_element<'a>( - count: &'a CriteriaGroups, - key1: &'a str, - key2: &'a str, - key3: &'a str, -) -> Option<&'a u64> { - count - .get(key1) +fn get_element<'a>(count: &'a CriteriaGroups, key1: &'a str, key2: &'a str, key3: &'a str) -> Option<&'a u64> { + count.get(key1) .and_then(|group| group.get(key2)) .and_then(|criteria| criteria.get(key3)) } + pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Value { debug!("Fetching catalogue from {catalogue_url} ..."); @@ -33,11 +27,11 @@ pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Value { .await .expect("Unable to fetch catalogue from upstream; please check URL specified in config."); - let mut json: Value = resp - .json() - .await + let mut json: Value = resp.json().await .expect("Unable to parse catalogue from upstream; please check URL specified in config."); +// tokio::time::sleep(Duration::from_secs(10)).await; + let prism_resp = reqwest::Client::new() .post(format!("{}criteria", prism_url)) .header("Content-Type", "application/json") @@ -47,9 +41,7 @@ pub async fn get_extended_json(catalogue_url: Url, prism_url: Url) -> Value { .await .expect("Unable to fetch response from Prism; please check it's running."); - let mut counts: CriteriaGroups = prism_resp - .json() - .await + let mut counts: CriteriaGroups = prism_resp.json().await .expect("Unable to parse response from Prism into CriteriaGroups"); recurse(&mut json, &mut counts); //TODO remove from counts once copied into catalogue to make it O(n log n) @@ -68,9 +60,10 @@ fn recurse(json: &mut Value, counts: &mut CriteriaGroups) { for ele in arr { recurse(ele, counts); } - } + }, Value::Object(obj) => { - if !obj.contains_key("childCategories") { + + if ! obj.contains_key("childCategories") { for (_key, child_val) in obj.iter_mut() { recurse(child_val, counts); } @@ -79,15 +72,10 @@ fn recurse(json: &mut Value, counts: &mut CriteriaGroups) { .expect("Got JSON where a criterion key was not a string. Please check json.").to_owned(); //TODO consolidate catalogue and MeasureReport group names - let group_key = if group_key == "patient" { - "patients" - } else if group_key == "tumor_classification" { - "diagnosis" - } else if group_key == "biosamples" { - "specimen" - } else { - &group_key - }; + let group_key = if group_key == "patient" {"patients"} + else if group_key == "tumor_classification" {"diagnosis"} + else if group_key == "biosamples" {"specimen"} + else {&group_key}; let children_cats = obj .get_mut("childCategories") @@ -96,7 +84,7 @@ fn recurse(json: &mut Value, counts: &mut CriteriaGroups) { .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.").as_str() .expect("Got JSON where a criterion key was not a string. Please check json.").to_owned(); @@ -108,32 +96,27 @@ fn recurse(json: &mut Value, counts: &mut CriteriaGroups) { .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 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."); - - let count_from_prism = - get_element(counts, &group_key, &stratifier_key, stratum_key); + + let count_from_prism = get_element(counts, &group_key, &stratifier_key, stratum_key); match count_from_prism { Some(count) => { criterion.insert("count".into(), json!(count)); - } + }, None => { - debug!( - "No count from Prism for {}, {}, {}", - group_key, stratifier_key, stratum_key - ); + debug!("No count from Prism for {}, {}, {}", group_key, stratifier_key, stratum_key); } - } + } } } } - } + }, _ => {} } -} +} \ No newline at end of file diff --git a/src/config.rs b/src/config.rs index c14e3db..5dbd051 100644 --- a/src/config.rs +++ b/src/config.rs @@ -34,7 +34,7 @@ pub struct Config { /// URL to catalogue.json file #[clap(long, env)] - pub catalogue_url: Url, + pub catalogue_url: Option, /// URL to prism #[clap(long, env, default_value= "http://localhost:8066")] diff --git a/src/main.rs b/src/main.rs index ae20f9d..ace0b20 100644 --- a/src/main.rs +++ b/src/main.rs @@ -47,29 +47,40 @@ async fn main() { info!("{:#?}", Lazy::force(&CONFIG)); - let extended_json = - catalogue::get_extended_json(CONFIG.catalogue_url.clone(), CONFIG.prism_url.clone()).await; - let state = SharedState { extended_json }; - - // TODO: Add check for reachability of beam-proxy - let cors = CorsLayer::new() .allow_methods([Method::GET, Method::POST]) .allow_origin(CONFIG.cors_origin.clone()) .allow_headers([header::CONTENT_TYPE]); - 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); + 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 state = SharedState { extended_json }; + + 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); + + app.into_make_service() + } else { + let app = Router::new() + .route("/beam", post(handle_create_beam_task)) + .route("/beam/:task_id", get(handle_listen_to_beam_tasks)) + .layer(axum::middleware::map_response(banner::set_server_header)) + .layer(cors); + + app.into_make_service() + }; + + // TODO: Add check for reachability of beam-proxy banner::print_banner(); axum::Server::bind(&CONFIG.bind_addr) - .serve(app.into_make_service()) + .serve(make_service) .await .unwrap(); } From 3e73141d0da4d0167028cb16552a655fc461d3da Mon Sep 17 00:00:00 2001 From: Enola Knezevic Date: Thu, 4 Apr 2024 15:00:02 +0200 Subject: [PATCH 2/3] version bump --- Cargo.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index 9887ff5..40aaa00 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "spot" -version = "0.2.0" +version = "0.3.0" edition = "2021" license = "Apache-2.0" documentation = "https://github.com/samply/spot" From 3e3d725e393921cf26eec5514b667426b0257d0f Mon Sep 17 00:00:00 2001 From: lablans Date: Thu, 4 Apr 2024 13:01:27 +0000 Subject: [PATCH 3/3] Version 0.2.1 --- Cargo.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index 40aaa00..616561d 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "spot" -version = "0.3.0" +version = "0.2.1" edition = "2021" license = "Apache-2.0" documentation = "https://github.com/samply/spot"