Merge pull request #1804 from samply/release/v0.27.1

Release v0.27.1

.github/scripts/search-tag.sh

@@ -0,0 +1,28 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+
+patient() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "meta": {
+    "tag": [
+      {
+        "system": "http://acme.org/codes",
+        "code": "needs-review"
+      }
+    ]
+  }
+}
+END
+}
+
+curl -s -f -H 'Content-Type: application/fhir+json' -H 'Accept: application/fhir+json' -d "$(patient)" -o /dev/null "$BASE/Patient"
+
+BUNDLE="$(curl -sH 'Accept: application/fhir+json' -H 'Prefer: handling=strict' "$BASE/Patient?_tag=http://acme.org/codes|needs-review")"
+
+test "tag of all resources" "$(echo "$BUNDLE" | jq -r '.entry[].resource.meta.tag[].code' | uniq)" "needs-review"

.github/workflows/build.yml

@@ -250,7 +250,7 @@ jobs:
       uses: docker/setup-buildx-action@d70bba72b1f3fd22344832f00baa16ece964efeb # v3
 
     - name: Build and Export to Docker
-      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5
+      uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25 # v5
       with:
         context: .
         tags: blaze:latest
@@ -282,7 +282,7 @@ jobs:
       uses: docker/setup-buildx-action@d70bba72b1f3fd22344832f00baa16ece964efeb # v3
 
     - name: Build and Export to Docker
-      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5
+      uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25 # v5
       with:
         context: modules/frontend
         tags: blaze-frontend:latest
@@ -329,7 +329,7 @@ jobs:
 
     - name: Upload Trivy Scan Results to GitHub Security Tab
       if: ${{ (github.repository_owner == 'samply') || (vars.IMAGE_SCAN_UPLOAD == 'true') }}
-      uses: github/codeql-action/upload-sarif@2e230e8fe0ad3a14a340ad0815ddb96d599d2aff # v3
+      uses: github/codeql-action/upload-sarif@23acc5c183826b7a8a97bce3cecc52db901f8251 # v3
       with:
         sarif_file: trivy-results.sarif
 
@@ -832,6 +832,9 @@ jobs:
     - name: Cancel Async Query
       run: .github/scripts/cancel-async.sh
 
+    - name: Search _tag
+      run: .github/scripts/search-tag.sh
+
     - name: Prometheus Metrics
       run: .github/scripts/test-metrics.sh
       if: ${{ matrix.variant == 'standalone' }}
@@ -1714,7 +1717,7 @@ jobs:
           type=semver,pattern={{major}}.{{minor}}
 
     - name: Build and push to GHCR
-      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5
+      uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25 # v5
       with:
         context: ${{ matrix.image.context }}
         platforms: linux/amd64,linux/arm64
@@ -1745,7 +1748,7 @@ jobs:
 
     - name: Build and push to DockerHub
       if: ${{ env.dockerhub_username != '' }}
-      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5
+      uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25 # v5
       with:
         context: ${{ matrix.image.context }}
         platforms: linux/amd64,linux/arm64

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.27.1
+
+### Enhancements
+
+* Enable FHIR Search by _tag ([#1801](https://github.com/samply/blaze/issues/1801))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/92?closed=1).
+
 ## v0.27.0
 
 ### New Features

Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && apt-get upgrade -y && \
     rm -rf /var/lib/apt/lists/
 
 RUN mkdir -p /app/data && chown 1001:1001 /app/data
-COPY target/blaze-0.27.0-standalone.jar /app/
+COPY target/blaze-0.27.1-standalone.jar /app/
 
 WORKDIR /app
 USER 1001
@@ -20,4 +20,4 @@ ENV RESOURCE_DB_DIR="/app/data/resource"
 ENV ADMIN_INDEX_DB_DIR="/app/data/admin-index"
 ENV ADMIN_TRANSACTION_DB_DIR="/app/data/admin-transaction"
 
-CMD ["java", "-jar",  "blaze-0.27.0-standalone.jar"]
+CMD ["java", "-jar",  "blaze-0.27.1-standalone.jar"]

README.md

@@ -19,7 +19,7 @@ A demo installation can be found [here](https://blaze.life.uni-leipzig.de/fhir)
 
 Blaze is widely used in the [Medical Informatics Initiative](https://www.medizininformatik-initiative.de) in Germany and in [Biobanks](https://www.bbmri-eric.eu) across Europe. A 1.0 version is expected in the next months.
 
-Latest release: [v0.27.0][5]
+Latest release: [v0.27.1][5]
 
 ## Quick Start
 
@@ -75,7 +75,7 @@ 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/v0.27.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.27.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

build.clj

@@ -2,7 +2,7 @@
   (:require [clojure.tools.build.api :as b]))
 
 (def lib 'samply/blaze)
-(def version "0.27.0")
+(def version "0.27.1")
 (def class-dir "target/classes")
 (def basis (b/create-basis {:project "deps.edn"}))
 (def uber-file (format "target/%s-%s-standalone.jar" (name lib) version))

docs/.vitepress/config.ts

@@ -27,7 +27,7 @@ export default defineConfig({
         nav: [
             {text: 'Home', link: '/'},
             {
-                text: "v0.27.0",
+                text: "v0.27.1",
                 items: [
                     {
                         text: 'Changelog',

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/v0.27.0). Look for `blaze-0.27.0-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/v0.27.1). Look for `blaze-0.27.1-standalone.jar`.
 
 After the download, you can start blaze with the following command (Linux, macOS):
 
 ```sh
-java -jar blaze-0.27.0-standalone.jar
+java -jar blaze-0.27.1-standalone.jar
 ```
 
 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-0.27.0-standalone.jar
+STORAGE=standalone java -jar blaze-0.27.1-standalone.jar
 ```
 
 Under Windows, you need to set the Environment variables in the PowerShell before starting Blaze:
 
 ```powershell
 $Env:STORAGE="standalone"
-java -jar blaze-0.27.0-standalone.jar
+java -jar blaze-0.27.1-standalone.jar
 ```
 
 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 0.27.0 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.27.1 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -62,7 +62,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.27.0"
+  "version": "0.27.1"
 }
 ```
 

docs/deployment/standalone-backend.md

@@ -27,7 +27,7 @@ Blaze should log something like this:
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:67] - JVM version: 17.0.7
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:68] - Maximum available memory: 1738 MiB
 2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:69] - Number of available processors: 2
-2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:70] - Successfully started 🔥 Blaze version 0.27.0 in 9.0 seconds
+2023-06-09T08:30:30.126Z b45689460ff3 main INFO [blaze.core:70] - Successfully started 🔥 Blaze version 0.27.1 in 9.0 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.27.0"
+  "version": "0.27.1"
 }
 ```
 

modules/cassandra/deps.edn

@@ -12,7 +12,7 @@
 
   ;; current version of transitive dependency of com.datastax.oss/java-driver-core
   io.netty/netty-handler
-  {:mvn/version "4.1.110.Final"}}
+  {:mvn/version "4.1.111.Final"}}
 
  :aliases
  {:test

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

@@ -4644,6 +4644,22 @@
           [0 :id] := "0"
           [1 :id] := "1")))))
 
+(deftest type-query-tag-test
+  (with-system-data [{:blaze.db/keys [node]} config]
+    [[[:put {:fhir/type :fhir/Patient :id "0"
+             :meta #fhir/Meta{:tag [#fhir/Coding{:code #fhir/code"code-084033"}]}}]
+      [:put {:fhir/type :fhir/Patient :id "1"}]
+      [:put {:fhir/type :fhir/Patient :id "2"
+             :meta #fhir/Meta{:tag [#fhir/Coding{:code #fhir/code"code-084517"}]}}]]]
+
+    (given (pull-type-query node "Patient" [["_tag" "code-084033"]])
+      count := 1
+      [0 :id] := "0")
+
+    (given (pull-type-query node "Patient" [["_tag" "code-084517"]])
+      count := 1
+      [0 :id] := "2")))
+
 (deftest compile-type-query-test
   (testing "a node with one patient"
     (with-system-data [{:blaze.db/keys [node]} config]