Merge pull request #550 from samply/release-v0.13.3

Release v0.13.3

.clj-kondo/config.edn

@@ -1,5 +1,5 @@
 {:lint-as
- {blaze.async.comp/do-sync clojure.core/let}
+ {blaze.test-util/with-system clojure.core/with-open}
 
  :linters
  {:unsorted-required-namespaces

.github/distributed-test/docker-compose.yml

@@ -82,6 +82,8 @@ services:
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
       DB_RESOURCE_CACHE_SIZE: "1000"
       LOG_LEVEL: "debug"
+    ports:
+    - "8081:8081"
     volumes:
     - "./blaze.keystore.jks:/app/blaze.keystore.jks:ro"
     - "./kafka.truststore.jks:/app/kafka.truststore.jks:ro"
@@ -109,6 +111,8 @@ services:
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
       DB_RESOURCE_CACHE_SIZE: "1000"
       LOG_LEVEL: "debug"
+    ports:
+    - "8082:8081"
     volumes:
     - "./blaze.keystore.jks:/app/blaze.keystore.jks:ro"
     - "./kafka.truststore.jks:/app/kafka.truststore.jks:ro"

.github/workflows/build.yml

@@ -64,6 +64,7 @@ jobs:
         - rocksdb
         - scheduler
         - search-param-registry
+        - server
         - thread-pool-executor-collector
 
         java-version:
@@ -133,6 +134,7 @@ jobs:
         - rocksdb
         - scheduler
         - search-param-registry
+        - server
         - thread-pool-executor-collector
 
     runs-on: ubuntu-20.04
@@ -326,7 +328,7 @@ jobs:
       run: docker pull ghcr.io/samply/blaze:sha-${{ github.sha }}
 
     - name: Run Blaze
-      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 -v blaze-data:/app/data ghcr.io/samply/blaze:sha-${{ github.sha }}
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 -p 8081:8081 -v blaze-data:/app/data ghcr.io/samply/blaze:sha-${{ github.sha }}
 
     - name: Sleep 60 Seconds
       run: sleep 60
@@ -448,6 +450,9 @@ jobs:
     - name: OPTIONS
       run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
 
+    - name: Prometheus Metrics
+      run: curl -f http://localhost:8081/metrics
+
   jepsen-test:
     needs: build
     runs-on: ubuntu-20.04
@@ -713,6 +718,12 @@ jobs:
     - name: OPTIONS
       run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
 
+    - name: Prometheus Metrics - Blaze 1
+      run: curl -f http://localhost:8081/metrics
+
+    - name: Prometheus Metrics - Blaze 2
+      run: curl -f http://localhost:8082/metrics
+
     - name: Docker Stats
       run: docker stats --no-stream
 

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## v0.13.3
+
+### Bugfixes
+
+* Fix Failing Metrics Endpoint ([#547](https://github.com/samply/blaze/pull/547))
+
+### Security
+
+* Fix CVE-2021-37137 in Package io.netty:netty-codec ([#548](https://github.com/samply/blaze/pull/548))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/18?closed=1).
+
 ## v0.13.2
 
 ### Security

deps.edn

@@ -25,6 +25,9 @@
   blaze/rocksdb
   {:local/root "modules/rocksdb"}
 
+  blaze/server
+  {:local/root "modules/server"}
+
   blaze/structure-definition
   {:local/root "modules/structure-definition"}
 
@@ -40,19 +43,8 @@
   org.clojure/tools.reader
   {:mvn/version "1.3.6"}
 
-  org.eclipse.jetty/jetty-server
-  {:mvn/version "9.4.44.v20210927"}
-
   org.slf4j/slf4j-nop
-  {:mvn/version "1.7.32"}
-
-  ring/ring-jetty-adapter
-  {:mvn/version "1.9.4"
-   :exclusions
-   [clj-time/clj-time
-    commons-fileupload/commons-fileupload
-    crypto-equality/crypto-equality
-    crypto-random/crypto-random]}}
+  {:mvn/version "1.7.32"}}
 
  :aliases
  {:depstar

docs/deployment/docker-deployment.md

@@ -27,7 +27,7 @@ Blaze should log something like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.2 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.3 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.13.2"
+  "version": "0.13.3"
 }
 ```
 

docs/deployment/manual-deployment.md

@@ -2,12 +2,12 @@
 
 The installation works under Windows, Linux and macOS. The only dependency is an installed OpenJDK 11. Blaze is tested with [AdoptOpenJDK][1].
 
-Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.13.1). Look for `blaze-0.13.2-standalone.jar`.
+Blaze runs on the JVM and comes as single JAR file. Download the most recent version [here](https://github.com/samply/blaze/releases/tag/v0.13.1). Look for `blaze-0.13.3-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.13.2-standalone.jar -m blaze.core
+java -jar blaze-0.13.3-standalone.jar -m blaze.core
 ```
 
 Blaze will run with an in-memory, volatile database for testing and demo purposes.
@@ -17,14 +17,14 @@ Blaze can be run with durable storage by setting the environment variables `STOR
 Under Linux/macOS:
 
 ```sh
-STORAGE=standalone java -jar blaze-0.13.2-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.13.3-standalone.jar -m blaze.core
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.13.2-standalone.jar -m blaze.core
+java -jar blaze-0.13.3-standalone.jar -m blaze.core
 ```
 
 This will create three directories called `index`, `transaction` and `resource` inside the current working directory, one for each database part used.
@@ -42,7 +42,7 @@ The output should look like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.2 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.3 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.13.2"
+  "version": "0.13.3"
 }
 ```
 

modules/anomaly/src/blaze/anomaly.clj

@@ -78,10 +78,14 @@
     (busy (.getMessage e)))
   ExceptionInfo
   (-anomaly [e]
-    (let [data (.getData e)]
-      (if (anomaly? data)
-        data
-        (fault (.getMessage e)))))
+    (cond->
+      (merge
+        (cond-> {::anom/category ::anom/fault}
+          (.getMessage e)
+          (assoc ::anom/message (.getMessage e)))
+        (.getData e))
+      (.getCause e)
+      (assoc :blaze.anomaly/cause (-anomaly (.getCause e)))))
   Throwable
   (-anomaly [e]
     (fault (.getMessage e)))

modules/anomaly/test/blaze/anomaly_test.clj

@@ -180,14 +180,28 @@
 
   (testing "ExceptionInfo"
     (testing "without an anomaly in data"
-      (given (ba/anomaly (ex-info "msg-184349" {}))
+      (given (ba/anomaly (ex-info "msg-184349" {::foo ::bar}))
         ::anom/category := ::anom/fault
-        ::anom/message := "msg-184349"))
+        ::anom/message := "msg-184349"
+        ::foo := ::bar))
 
     (testing "with an anomaly in data"
       (given (ba/anomaly (ex-info "msg-184349" (ba/incorrect "msg-184433")))
         ::anom/category := ::anom/incorrect
-        ::anom/message := "msg-184433")))
+        ::anom/message := "msg-184433"))
+
+    (testing "without message"
+      (is (= ::none ((ba/anomaly (ex-info nil {})) ::anom/message ::none))))
+
+    (testing "with cause"
+      (given (ba/anomaly (ex-info "msg-181247" {} (Exception. "msg-181120")))
+        ::anom/message := "msg-181247"
+        [:blaze.anomaly/cause ::anom/message] := "msg-181120")
+
+      (testing "and nil message"
+        (given (ba/anomaly (ex-info "msg-181247" {} (Exception.)))
+          ::anom/message := "msg-181247"
+          [:blaze.anomaly/cause #(% ::anom/message ::none)] := ::none))))
 
   (testing "Exception"
     (given (ba/anomaly (Exception. "msg-120840"))
@@ -203,7 +217,7 @@
 (deftest try-one-test
   (testing "without message"
     (is (= (ba/try-one Exception ::anom/fault (throw (Exception.)))
-         {::anom/category ::anom/fault})))
+           {::anom/category ::anom/fault})))
 
   (testing "with message"
     (given (ba/try-one Exception ::anom/fault (throw (Exception. "msg-134156")))

modules/cassandra/deps.edn

@@ -6,7 +6,11 @@
   {:mvn/version "0.3.3"}
 
   com.datastax.oss/java-driver-core
-  {:mvn/version "4.13.0"}}
+  {:mvn/version "4.13.0"}
+
+  ;; curreny version of transitive dependency of com.datastax.oss/java-driver-core
+  io.netty/netty-handler
+  {:mvn/version "4.1.70.Final"}}
 
  :aliases
  {:test

src/blaze/handler/metrics.clj → modules/metrics/src/blaze/metrics/handler.clj

@@ -1,4 +1,4 @@
-(ns blaze.handler.metrics
+(ns blaze.metrics.handler
   (:require
     [blaze.metrics.spec]
     [clojure.spec.alpha :as s]
@@ -7,11 +7,11 @@
     [taoensso.timbre :as log]))
 
 
-(defmethod ig/pre-init-spec :blaze.handler/metrics [_]
+(defmethod ig/pre-init-spec :blaze.metrics/handler [_]
   (s/keys :req-un [:blaze.metrics/registry]))
 
 
-(defmethod ig/init-key :blaze.handler/metrics
+(defmethod ig/init-key :blaze.metrics/handler
   [_ {:keys [registry]}]
   (log/info "Init metrics handler")
   (fn [_]

modules/metrics/src/blaze/metrics/registry.clj

@@ -17,7 +17,7 @@
 
 
 (defmethod ig/pre-init-spec :blaze.metrics/registry [_]
-  (s/keys :req-un [:blaze.metrics/collectors]))
+  (s/keys :opt-un [:blaze.metrics/collectors]))
 
 
 (defn- register-collectors! [registry collectors]
@@ -29,7 +29,7 @@
 
 
 (defmethod ig/init-key :blaze.metrics/registry
-  [_ {:keys [collectors]}]
+  [_ {:keys [collectors] :or {collectors []}}]
   (log/info "Init metrics registry")
   (doto (CollectorRegistry. true)
     (.register (StandardExports.))

modules/metrics/src/blaze/metrics/spec.clj

@@ -13,8 +13,12 @@
   (s/coll-of :blaze.metrics/collector))
 
 
+(defn registry? [x]
+  (instance? CollectorRegistry x))
+
+
 (s/def :blaze.metrics/registry
-  #(instance? CollectorRegistry %))
+  registry?)
 
 
 (s/def :blaze.metrics/metric

modules/metrics/test/blaze/metrics/handler_test.clj

@@ -0,0 +1,60 @@
+(ns blaze.metrics.handler-test
+  (:require
+    [blaze.metrics.handler]
+    [blaze.metrics.registry]
+    [blaze.metrics.spec :as spec]
+    [blaze.test-util :refer [given-thrown with-system]]
+    [clojure.spec.alpha :as s]
+    [clojure.spec.test.alpha :as st]
+    [clojure.string :as str]
+    [clojure.test :as test :refer [deftest testing]]
+    [integrant.core :as ig]
+    [juxt.iota :refer [given]]
+    [taoensso.timbre :as log]))
+
+
+(st/instrument)
+(log/set-level! :trace)
+
+
+(defn- fixture [f]
+  (st/instrument)
+  (f)
+  (st/unstrument))
+
+
+(test/use-fixtures :each fixture)
+
+
+(deftest init-test
+  (testing "nil config"
+    (given-thrown (ig/init {:blaze.metrics/handler nil})
+      :key := :blaze.metrics/handler
+      :reason := ::ig/build-failed-spec
+      [:explain ::s/problems 0 :pred] := `map?))
+
+  (testing "missing config"
+    (given-thrown (ig/init {:blaze.metrics/handler {}})
+      :key := :blaze.metrics/handler
+      :reason := ::ig/build-failed-spec
+      [:explain ::s/problems 0 :pred] := `(fn ~'[%] (contains? ~'% :registry))))
+
+  (testing "invalid registry"
+    (given-thrown (ig/init {:blaze.metrics/handler {:registry ::invalid}})
+      :key := :blaze.metrics/handler
+      :reason := ::ig/build-failed-spec
+      [:explain ::s/problems 0 :pred] := `spec/registry?
+      [:explain ::s/problems 0 :val] := ::invalid)))
+
+
+(def system
+  {:blaze.metrics/handler {:registry (ig/ref :blaze.metrics/registry)}
+   :blaze.metrics/registry {}})
+
+
+(deftest handler-test
+  (with-system [{:blaze.metrics/keys [handler]} system]
+    (given (handler nil)
+      :status := 200
+      [:headers "Content-Type"] := "text/plain; version=0.0.4; charset=utf-8"
+      :body :? #(str/starts-with? % "# HELP"))))