Merge pull request #686 from samply/release-v0.16.5

Release v0.16.5
samply · Apr 24, 2022 · 7afce77 · 7afce77
2 parents df976c5 + a36b802
commit 7afce77
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diff --git a/.clj-kondo/config.edn b/.clj-kondo/config.edn
@@ -4,7 +4,11 @@
  :linters
  {:unsorted-required-namespaces
   {:level :error}
+
   :single-key-in
-  {:level :warning}}
+  {:level :warning}
+
+  :keyword-binding
+  {:level :error}}
 
  :skip-comments true}
diff --git a/.github/scripts/include-without-referential-integrity.sh b/.github/scripts/include-without-referential-integrity.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -e
+
+BASE="http://localhost:8080/fhir"
+
+curl -sXPUT -d '{"resourceType": "Observation", "id": "0", "subject": {"reference": "Patient/0"}}' -H 'Content-Type: application/fhir+json' "$BASE/Observation/0" > /dev/null
+curl -sXPUT -d '{"resourceType" : "Patient", "id": "0"}' -H 'Content-Type: application/fhir+json' "$BASE/Patient/0" > /dev/null
+
+RESULT=$(curl -s "$BASE/Observation?_include=Observation:subject" | jq -r '.entry[].search.mode' | tr '\n' '|')
+
+if [ "$RESULT" = "match|include|" ]; then
+  echo "Success: include works"
+else
+  echo "Fail: include doesn't work"
+  exit 1
+fi
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -22,7 +22,7 @@ jobs:
     - name: Setup clj-kondo
       uses: DeLaGuardo/setup-clj-kondo@master
       with:
-        version: '2022.03.09'
+        version: '2022.04.23'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -38,6 +38,7 @@ jobs:
         module:
         - anomaly
         - async
+        - byte-buffer
         - cassandra
         - coll
         - cql
@@ -84,13 +85,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ matrix.module }}-${{ hashFiles(format('modules/{0}/deps.edn', matrix.module)) }}
@@ -115,13 +116,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-17-maven-test-coverage-${{ hashFiles('**/deps.edn') }}
@@ -130,7 +131,7 @@ jobs:
       run: make test-coverage
 
     - name: Codecov Upload
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         name: codecov-umbrella
         file: modules/**/target/coverage/codecov.json
@@ -157,13 +158,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ hashFiles('deps.edn') }}
@@ -185,13 +186,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-17-maven-build-${{ hashFiles('**/deps.edn') }}
@@ -538,6 +539,33 @@ jobs:
     - name: Load Data with Concurrency 2
       run: blazectl --no-progress --server http://localhost:8080/fhir upload -c 2 .github/test-data/small-txs
 
+  include-without-referential-integrity-test:
+    needs: build
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v3
+
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v1
+      with:
+        registry: ghcr.io
+        username: ${{ github.repository_owner }}
+        password: ${{ secrets.CR_PAT }}
+
+    - name: Pull Docker Image
+      run: docker pull ghcr.io/samply/blaze:sha-${{ github.sha }}
+
+    - name: Run Blaze
+      run: docker run --rm -d -e JAVA_TOOL_OPTIONS=-Xmx1g -e ENFORCE_REFERENTIAL_INTEGRITY=false -p 8080:8080 ghcr.io/samply/blaze:sha-${{ github.sha }}
+
+    - name: Wait for Blaze
+      run: .github/scripts/wait-for-url.sh  http://localhost:8080/health
+
+    - name: Test Include
+      run: .github/scripts/include-without-referential-integrity.sh
+
   jepsen-test:
     needs: build
     runs-on: ubuntu-20.04
@@ -552,13 +580,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}
@@ -854,13 +882,13 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        tools-deps: '1.10.3.1087'
+        cli: '1.11.1.1113'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
 
     - name: Cache Local Maven Repo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,14 @@
 
 ### Security
 
+* Update Jackson Databind to v2.13.2.2 ([#668](https://github.com/samply/blaze/pull/668))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/35?closed=1).
+
+## v0.16.4
+
+### Security
+
 * Update Jackson Databind to v2.13.2.1 ([#659](https://github.com/samply/blaze/pull/659))
 * Remove Unused Oracle Linux Packages ([#653](https://github.com/samply/blaze/pull/653))
 

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Blaze
 
-[![Build Status](https://github.com/samply/blaze/workflows/Build/badge.svg)](https://github.com/samply/blaze/actions?query=workflow%3ABuild)
+[![Build](https://github.com/samply/blaze/actions/workflows/build.yml/badge.svg)](https://github.com/samply/blaze/actions/workflows/build.yml)
 [![Docker Pulls](https://img.shields.io/docker/pulls/samply/blaze.svg)](https://hub.docker.com/r/samply/blaze/)
 [![codecov](https://codecov.io/gh/samply/blaze/branch/develop/graph/badge.svg)](https://codecov.io/gh/samply/blaze)
 
@@ -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: [v0.16.4][5]
+Latest release: [v0.16.5][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/v0.16.4>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.16.5>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>