Merge pull request #719 from samply/release-v0.17.4

Release v0.17.4

.github/workflows/build.yml

@@ -200,34 +200,28 @@ jobs:
     - name: Build Uberjar
       run: make uberjar
 
-    - name: Set up QEMU
-      uses: docker/setup-qemu-action@v1
-
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
-
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.CR_PAT }}
 
     - name: Login to DockerHub
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v1
+      uses: docker/setup-qemu-action@v2
 
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
+      uses: docker/setup-buildx-action@v2
 
     - name: Docker meta
       id: docker-meta
-      uses: docker/metadata-action@v3
+      uses: docker/metadata-action@v4
       with:
         images: |
           samply/blaze
@@ -241,7 +235,7 @@ jobs:
           type=sha,format=long
 
     - name: Build and push
-      uses: docker/build-push-action@v2
+      uses: docker/build-push-action@v3
       with:
         context: .
         platforms: linux/amd64,linux/arm64
@@ -274,7 +268,7 @@ jobs:
       run: .github/scripts/install-blazectl.sh
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -478,7 +472,7 @@ jobs:
       run: .github/scripts/install-blazectl.sh
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -524,7 +518,7 @@ jobs:
       run: .github/scripts/install-blazectl.sh
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -563,7 +557,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -613,7 +607,7 @@ jobs:
       run: sudo apt-get install gnuplot
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -646,7 +640,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -682,7 +676,7 @@ jobs:
       run: .github/scripts/install-blazectl.sh
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -930,7 +924,7 @@ jobs:
       run: sudo apt-get install gnuplot
 
     - name: Login to GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.17.4
+
+### Bugfixes
+
+* Return an Error on Incorrect Content-Type for Search Requests ([#524](https://github.com/samply/blaze/issues/524))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/42?closed=1).
+
 ## v0.17.3
 
 ### Bugfixes

README.md

@@ -14,7 +14,7 @@ The goal of this project is to provide a FHIR® Store with an internal CQL Evalu
 
 Blaze passes all [Touchstone FHIR 4.0.1 Basic Tests][12] and almost all [CQL Tests][3]. Please refer to the [Conformance](docs/conformance.md) section and report any issues you encounter during evaluation.
 
-Latest release: [v0.17.3][5]
+Latest release: [v0.17.4][5]
 
 ## Quick Start
 
@@ -72,7 +72,7 @@ Unless required by applicable law or agreed to in writing, software distributed
 
 [3]: <https://cql.hl7.org/tests.html>
 [4]: <https://alexanderkiel.gitbook.io/blaze/deployment>
-[5]: <https://github.com/samply/blaze/releases/tag/v0.17.3>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.17.4>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

deps.edn

@@ -61,7 +61,7 @@
     {:mvn/version "0.4.6"}
 
     org.clojure/tools.namespace
-    {:mvn/version "1.2.0"}}}
+    {:mvn/version "1.3.0"}}}
 
   :kaocha
   {:extra-deps
@@ -75,12 +75,12 @@
 
    :extra-deps
    {org.clojure/tools.namespace
-    {:mvn/version "1.2.0"}}}
+    {:mvn/version "1.3.0"}}}
 
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "1.6.1"}
+    {:mvn/version "1.6.2"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "1.7.36"}}

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 0.17.3 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.4 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.3"
+  "version": "0.17.4"
 }
 ```
 

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/v0.17.3). Look for `blaze-0.17.3-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/v0.17.4). Look for `blaze-0.17.4-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.17.3-standalone.jar -m blaze.core
+java -jar blaze-0.17.4-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-0.17.3-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.17.4-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-0.17.3-standalone.jar -m blaze.core
+java -jar blaze-0.17.4-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 0.17.3 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.17.4 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.17.3"
+  "version": "0.17.4"
 }
 ```
 

modules/byte-string/deps.edn

@@ -8,4 +8,4 @@
   {:mvn/version "3.20.1"}
 
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.13.2.2"}}}
+  {:mvn/version "2.13.3"}}}

modules/cassandra/deps.edn

@@ -7,11 +7,11 @@
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   com.fasterxml.jackson.core/jackson-databind
-  {:mvn/version "2.13.2.2"}
+  {:mvn/version "2.13.3"}
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   io.netty/netty-handler
-  {:mvn/version "4.1.76.Final"}}
+  {:mvn/version "4.1.77.Final"}}
 
  :aliases
  {:test

modules/cql/deps.edn

@@ -5,7 +5,7 @@
   {:local/root "../db"}
 
   com.fasterxml.jackson.module/jackson-module-jaxb-annotations
-  {:mvn/version "2.13.2"}
+  {:mvn/version "2.13.3"}
 
   info.cqframework/cql-to-elm
   {:mvn/version "1.5.8"

modules/db-stub/src/blaze/db/api_stub.clj

@@ -16,8 +16,7 @@
     [blaze.db.tx-log.local]
     [blaze.fhir.structure-definition-repo]
     [blaze.test-util :refer [with-system]]
-    [integrant.core :as ig]
-    [java-time :as time]))
+    [integrant.core :as ig]))
 
 
 (defn create-mem-node-system [node-config]
@@ -30,8 +29,7 @@
       :resource-store (ig/ref :blaze.db/resource-store)
       :kv-store (ig/ref :blaze.db/index-kv-store)
       :resource-indexer (ig/ref :blaze.db.node/resource-indexer)
-      :search-param-registry (ig/ref :blaze.db/search-param-registry)
-      :poll-timeout (time/millis 10)}
+      :search-param-registry (ig/ref :blaze.db/search-param-registry)}
      node-config)
 
    ::tx-log/local

modules/db-tx-log-kafka/deps.edn

@@ -15,7 +15,7 @@
   {:local/root "../module-base"}
 
   org.apache.kafka/kafka-clients
-  {:mvn/version "3.1.0"}}
+  {:mvn/version "3.2.0"}}
 
  :aliases
  {:test

modules/db/test/blaze/db/api_test.clj

@@ -1,7 +1,7 @@
 (ns blaze.db.api-test
   "Main high-level test of all database API functions."
   (:require
-    [blaze.anomaly :refer [when-ok]]
+    [blaze.anomaly :as ba :refer [when-ok]]
     [blaze.anomaly-spec]
     [blaze.async.comp :as ac]
     [blaze.async.comp-spec]
@@ -482,7 +482,7 @@
     (with-redefs
       [resource-indexer/index-resources
        (fn [_ _]
-         (ac/failed-future (ex-info "" {::anom/category ::anom/fault ::x ::y})))]
+         (ac/failed-future (ex-info "" (ba/fault "" ::x ::y))))]
       (with-system [{:blaze.db/keys [node]} system]
         (given-failed-future
           (d/transact node [[:put {:fhir/type :fhir/Patient :id "0"}]])

modules/db/test/blaze/db/node_test.clj

@@ -1,5 +1,6 @@
 (ns blaze.db.node-test
   (:require
+    [blaze.anomaly :as ba]
     [blaze.async.comp :as ac]
     [blaze.async.comp-spec]
     [blaze.db.api :as d]
@@ -179,7 +180,7 @@
       (with-redefs
         [resource-indexer/index-resources
          (fn [_ _]
-           (ac/failed-future (ex-info "" {::anom/category ::anom/fault ::x ::y})))]
+           (ac/failed-future (ex-info "" (ba/fault "" ::x ::y))))]
 
         (testing "fetching the result immediately"
           (with-system [{:blaze.db/keys [node]} resource-store-slow-on-put]

modules/fhir-structure/deps.edn

@@ -20,7 +20,7 @@
   {:mvn/version "31.1-jre"}
 
   com.fasterxml.jackson.dataformat/jackson-dataformat-cbor
-  {:mvn/version "2.13.2"}
+  {:mvn/version "2.13.3"}
 
   com.taoensso/timbre
   {:mvn/version "5.2.1"}

modules/fhir-structure/src/blaze/fhir/spec/impl.clj

@@ -403,7 +403,7 @@
 
 (defn- remap-choice-conformer-form
   "Creates a conformer form which removes the type suffix of keys on conforming
-  and adds it back on unforming."
+  and adds it back on uniforming."
   [[internal-key child-spec-defs]]
   `(s/conformer
      (fn [~'m]
@@ -499,8 +499,8 @@
 (defn conform-xml
   "First step in conforming an XML `element` into the internal form.
 
-  Builds a map from child tags to either vector of childs or single-valued
-  childs."
+  Builds a map from child tags to either vector of children or single-valued
+  children."
   {:arglists '([element])}
   [{:keys [attrs content]}]
   (transduce
@@ -583,8 +583,8 @@
 (defn- special-xml-schema-spec-form [kind type-name child-spec-defs]
   (let [constructor-sym (symbol "blaze.fhir.spec.type" (str "map->" type-name))
         constructor (resolve constructor-sym)]
-    (conj (seq (remap-choice-conformer-forms child-spec-defs))
-          `(s/conformer ~constructor identity)
+    (conj (seq (conj (remap-choice-conformer-forms child-spec-defs)
+                     `(s/conformer ~constructor identity)))
           (schema-spec-form :xml child-spec-defs)
           `(s/conformer conform-xml
                         ~(xml-unformer kind (keyword type-name) child-spec-defs))