Merge pull request #825 from samply/release-v0.18.2

Release v0.18.2
samply · Oct 25, 2022 · ffe6102 · ffe6102
2 parents 315385a + 8629c95
commit ffe6102
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diff --git a/.github/test-data/bundle-with-references/bundle.json b/.github/test-data/bundle-with-references/bundle.json
@@ -0,0 +1,30 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "resource": {
+        "resourceType": "Bundle",
+        "type": "transaction",
+        "entry": [
+          {
+            "resource": {
+              "resourceType": "Condition",
+              "subject": {
+                "reference": "Patient/db03f428-4fea-4006-bb90-aeaa7c6e9d1d"
+              }
+            },
+            "request": {
+              "method": "POST",
+              "url": "Condition"
+            }
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Bundle"
+      }
+    }
+  ]
+}
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -85,7 +85,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -116,7 +116,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -158,7 +158,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -186,7 +186,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -601,6 +601,37 @@ jobs:
     - name: Test Include
       run: .github/scripts/include-without-referential-integrity.sh
 
+  # Test that a transaction can create a transaction bundle with references that will be taken "as-is" and not tried to
+  # resolve to existing resources
+  bundle-with-references-test:
+    needs: build
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v3
+
+    - name: Install Blazectl
+      run: .github/scripts/install-blazectl.sh
+
+    - name: Download Blaze Image
+      uses: actions/download-artifact@v3
+      with:
+        name: blaze-image
+        path: /tmp
+
+    - name: Load Blaze Image
+      run: docker load --input /tmp/blaze.tar
+
+    - name: Run Blaze
+      run: docker run --rm -d -e JAVA_TOOL_OPTIONS=-Xmx1g -p 8080:8080 blaze:latest
+
+    - name: Wait for Blaze
+      run: .github/scripts/wait-for-url.sh  http://localhost:8080/health
+
+    - name: Load Data
+      run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/bundle-with-references
+
   jepsen-test:
     needs: build
     runs-on: ubuntu-20.04
@@ -615,7 +646,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3
@@ -950,7 +981,7 @@ jobs:
     - name: Setup Clojure
       uses: DeLaGuardo/setup-clojure@master
       with:
-        cli: '1.11.1.1165'
+        cli: '1.11.1.1182'
 
     - name: Check out Git repository
       uses: actions/checkout@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # Changelog
 
+## v0.18.2
+
+### Bugfixes
+
+* Fix Storage of Bundles with References ([#822](https://github.com/samply/blaze/pull/822))
+
+### Security
+
+* Update Dependencies ([#824](https://github.com/samply/blaze/pull/824))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/53?closed=1).
+
 ## v0.18.1
 
 ### Security

diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ 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: [v0.18.1][5]
+Latest release: [v0.18.2][5]
 
 ## Quick Start
 
@@ -73,7 +73,7 @@ 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/v0.18.1>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.18.2>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

diff --git a/deps.edn b/deps.edn
@@ -66,7 +66,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 
@@ -80,7 +80,7 @@
   :outdated
   {:replace-deps
    {com.github.liquidz/antq
-    {:mvn/version "2.1.932"}
+    {:mvn/version "2.1.939"}
 
     org.slf4j/slf4j-nop
     {:mvn/version "2.0.3"}}

diff --git a/docs/deployment/docker-deployment.md b/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 0.18.1 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.18.2 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.18.1"
+  "version": "0.18.2"
 }
 ```
 

diff --git a/docs/deployment/manual-deployment.md b/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 or 17 with 17 recommended. Blaze is tested with [Eclipse Temurin][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/v0.18.1). Look for `blaze-0.18.1-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/v0.18.2). Look for `blaze-0.18.2-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.18.1-standalone.jar -m blaze.core
+java -jar blaze-0.18.2-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-0.18.1-standalone.jar -m blaze.core
+STORAGE=standalone java -jar blaze-0.18.2-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-0.18.1-standalone.jar -m blaze.core
+java -jar blaze-0.18.2-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 0.18.1 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.18.2 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.18.1"
+  "version": "0.18.2"
 }
 ```
 

diff --git a/modules/anomaly/deps.edn b/modules/anomaly/deps.edn
@@ -16,7 +16,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/async/deps.edn b/modules/async/deps.edn
@@ -19,7 +19,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/byte-buffer/deps.edn b/modules/byte-buffer/deps.edn
@@ -1,6 +1,6 @@
 {:deps
  {com.google.protobuf/protobuf-java
-  {:mvn/version "3.21.7"}}
+  {:mvn/version "3.21.8"}}
 
  :aliases
  {:test
@@ -13,6 +13,6 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}}}
diff --git a/modules/byte-string/deps.edn b/modules/byte-string/deps.edn
@@ -5,7 +5,7 @@
   {:mvn/version "31.1-jre"}
 
   com.google.protobuf/protobuf-java
-  {:mvn/version "3.21.7"}
+  {:mvn/version "3.21.8"}
 
   com.fasterxml.jackson.core/jackson-databind
   {:mvn/version "2.13.4.2"}}}
diff --git a/modules/cassandra/deps.edn b/modules/cassandra/deps.edn
@@ -27,7 +27,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/coll/deps.edn b/modules/coll/deps.edn
@@ -8,7 +8,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/cql/deps.edn b/modules/cql/deps.edn
@@ -42,7 +42,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/db-resource-store-cassandra/deps.edn b/modules/db-resource-store-cassandra/deps.edn
@@ -25,7 +25,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/db-resource-store/deps.edn b/modules/db-resource-store/deps.edn
@@ -34,7 +34,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/db-tx-log-kafka/deps.edn b/modules/db-tx-log-kafka/deps.edn
@@ -28,7 +28,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/db-tx-log/deps.edn b/modules/db-tx-log/deps.edn
@@ -22,7 +22,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/db/deps.edn b/modules/db/deps.edn
@@ -52,7 +52,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/executor/deps.edn b/modules/executor/deps.edn
@@ -9,7 +9,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/extern-terminology-service/deps.edn b/modules/extern-terminology-service/deps.edn
@@ -22,7 +22,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/fhir-client/deps.edn b/modules/fhir-client/deps.edn
@@ -31,7 +31,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}
 

diff --git a/modules/fhir-path/deps.edn b/modules/fhir-path/deps.edn
@@ -19,7 +19,7 @@
   :kaocha
   {:extra-deps
    {lambdaisland/kaocha
-    {:mvn/version "1.70.1086"}}
+    {:mvn/version "1.71.1119"}}
 
    :main-opts ["-m" "kaocha.runner"]}