Release v0.30.1

samply · Oct 10, 2024 · f23b13a · f23b13a
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diff --git a/.github/distributed-test/docker-compose.yml b/.github/distributed-test/docker-compose.yml
@@ -125,6 +125,8 @@ services:
       DB_RESOURCE_CACHE_SIZE: "100000"
       DB_RESOURCE_INDEXER_THREADS: "8"
       ALLOW_MULTIPLE_DELETE: "true"
+      ENABLE_INTERACTION_DELETE_HISTORY: "true"
+      ENABLE_OPERATION_PATIENT_PURGE: "true"
     ports:
     - "8081:8081"
     volumes:
@@ -156,6 +158,8 @@ services:
       DB_RESOURCE_CACHE_SIZE: "100000"
       DB_RESOURCE_INDEXER_THREADS: "8"
       ALLOW_MULTIPLE_DELETE: "true"
+      ENABLE_INTERACTION_DELETE_HISTORY: "true"
+      ENABLE_OPERATION_PATIENT_PURGE: "true"
     ports:
     - "8082:8081"
     volumes:

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -293,7 +293,7 @@ jobs:
       uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
       with:
         path: ~/.m2/repository
-        key: ${{ runner.os }}-temurin-17-maven-build-${{ hashFiles('**/deps.edn') }}
+        key: ${{ runner.os }}-temurin-21-maven-build-${{ hashFiles('**/deps.edn') }}
 
     - name: Download Job IG Profiles
       uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
@@ -575,7 +575,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Blaze
-      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ALLOW_MULTIPLE_DELETE=true -p 8080:8080 -p 8081:8081 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ALLOW_MULTIPLE_DELETE=true -e ENABLE_INTERACTION_DELETE_HISTORY=true -e ENABLE_OPERATION_PATIENT_PURGE=true -p 8080:8080 -p 8081:8081 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
       if: ${{ matrix.variant == 'standalone' }}
 
     - name: Run Kafka, Cassandra and Blaze
@@ -1475,7 +1475,7 @@ jobs:
       uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
       with:
         path: ~/.m2/repository
-        key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}
+        key: ${{ runner.os }}-temurin-21-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}
 
     - name: APT Update
       run: sudo apt-get update
@@ -1493,7 +1493,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Blaze
-      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENABLE_INTERACTION_DELETE_HISTORY=true -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
 
     - name: Wait for Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
@@ -1867,7 +1867,7 @@ jobs:
       uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4
       with:
         path: ~/.m2/repository
-        key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}
+        key: ${{ runner.os }}-temurin-21-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }}
 
     - name: APT Update
       run: sudo apt-get update

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,18 @@
 # Changelog
 
+## v0.30.1
+
+### Bugfixes
+
+* Fix Returning Resources with Non-Matching Identifier ([#2111](https://github.com/samply/blaze/issues/2111))
+
+### Enhancements (alpha)
+
+* Implement the delete-history Command ([#1382](https://github.com/samply/blaze/issues/1382)) ([docs](https://github.com/samply/blaze/blob/main/docs/api.md#delete-history))
+* Implement Operation $purge on Patient ([#1298](https://github.com/samply/blaze/issues/1298)) ([docs](https://github.com/samply/blaze/blob/main/docs/api/operation-patient-purge.md))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/99?closed=1).
+
 ## v0.30.0
 
 ### Enhancements

diff --git a/Dockerfile b/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-0.30.0-standalone.jar /app/
+COPY target/blaze-0.30.1-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-0.30.0-standalone.jar"]
+CMD ["java", "-jar",  "blaze-0.30.1-standalone.jar"]
diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ 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: [v0.30.0][5]
+Latest release: [v0.30.1][5]
 
 ## Quick Start
 
@@ -76,7 +76,7 @@ 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/v0.30.0>
+[5]: <https://github.com/samply/blaze/releases/tag/v0.30.1>
 [6]: <https://www.yourkit.com/java/profiler/>
 [7]: <https://www.yourkit.com/.net/profiler/>
 [8]: <https://www.yourkit.com/youmonitor/>

diff --git a/build.clj b/build.clj
@@ -5,7 +5,7 @@
    [java.time LocalDate]))
 
 (def lib 'samply/blaze)
-(def version "0.30.0")
+(def version "0.30.1")
 (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))

diff --git a/docs/.vitepress/config.ts b/docs/.vitepress/config.ts
@@ -27,7 +27,7 @@ export default defineConfig({
         nav: [
             {text: 'Home', link: '/'},
             {
-                text: "v0.30.0",
+                text: "v0.30.1",
                 items: [
                     {
                         text: 'Changelog',

diff --git a/docs/api.md b/docs/api.md
@@ -52,6 +52,9 @@ By default Blaze enforces referential integrity while deleting resources. So res
 
 ### Delete History
 
+> [!CAUTION]
+> The delete history interaction is currently **alpha** and has to be enabled explicitly by setting the env var `ENABLE_INTERACTION_DELETE_HISTORY` to true. Please don't use it in production. Please be aware that the database might not be able to migrate to a newer version of Blaze if the operation was used.
+
 > [!CAUTION]
 > The delete history interaction is trial use in the unreleased next version of FHIR. So it is subject to change. Please use it with care.
 

diff --git a/docs/api/operation-patient-purge.md b/docs/api/operation-patient-purge.md
@@ -1,7 +1,10 @@
-# Operation Patient Purge
+# Operation \$purge on Patient
 
 > [!CAUTION]
-> The patient $purge operation is trial use in the unreleased next version of FHIR. So it is subject to change. Please use it with care.
+> The operation \$purge on patient is currently **alpha** and has to be enabled explicitly by setting the env var `ENABLE_OPERATION_PATIENT_PURGE` to true. Please don't use it in production. Please be aware that the database might not be able to migrate to a newer version of Blaze if the operation was used.
+
+> [!CAUTION]
+> The operation \$purge on patient is trial use in the unreleased next version of FHIR (R6). So it is subject to change. Please use it with care.
 
 The patient \$purge operation is used to request the removal of all current and historical versions for all resources in a patient compartment. The return is an OperationOutcome with results and/or details about execution. The `code` of the first issue of the OperationOutcome is either `success` on successful purging of all resources or an error.
 

diff --git a/docs/deployment/environment-variables.md b/docs/deployment/environment-variables.md
@@ -86,34 +86,36 @@ More information about distributed deployment are available [here](distributed-b
 
 ### Other Environment Variables
 
-| Name                                    | Default                    | Since  | Depr ¹ | Description                                                                                                 |
-|:----------------------------------------|:---------------------------|:-------|--------|:------------------------------------------------------------------------------------------------------------|
-| PROXY_HOST                              | —                          | v0.6   | —      | REMOVED: use -Dhttp.proxyHost                                                                               |
-| PROXY_PORT                              | —                          | v0.6   | —      | REMOVED: use -Dhttp.proxyPort                                                                               |
-| PROXY_USER                              | —                          | v0.6.1 | —      | REMOVED: try [SOCKS Options][1]                                                                             |
-| PROXY_PASSWORD                          | —                          | v0.6.1 | —      | REMOVED: try [SOCKS Options][1]                                                                             |
-| CONNECTION_TIMEOUT                      | 5 s                        | v0.6.3 | —      | connection timeout for outbound HTTP requests                                                               |
-| REQUEST_TIMEOUT                         | 30 s                       | v0.6.3 | —      | REMOVED                                                                                                     |
-| TERM_SERVICE_URI                        | [http://tx.fhir.org/r4][6] | v0.6   | v0.11  | Base URI of the terminology service                                                                         |
-| BASE_URL                                | `http://localhost:8080`    | —      | —      | The URL under which Blaze is accessible by clients.                                                         |
-| CONTEXT_PATH                            | /fhir                      | v0.11  | —      | Context path under which the FHIR RESTful API will be accessible.                                           |
-| SERVER_PORT                             | 8080                       | —      | —      | The port of the main HTTP server                                                                            |
-| METRICS_SERVER_PORT                     | 8081                       | v0.6   | —      | The port of the Prometheus metrics server                                                                   |
-| LOG_LEVEL                               | info                       | v0.6   | —      | one of trace, debug, info, warn or error                                                                    |
-| JAVA_TOOL_OPTIONS                       | —                          | —      | —      | JVM options \(Docker only\)                                                                                 |
-| FHIR_OPERATION_EVALUATE_MEASURE_THREADS | number of CPUs             | v0.8   | —      | The number threads used for $evaluate-measure executions.                                                   |
-| FHIR_OPERATION_EVALUATE_MEASURE_TIMEOUT | 3600000 (1h)               | v0.19  | —      | Timeout in milliseconds for synchronous $evaluate-measure executions.                                       |
-| OPENID_PROVIDER_URL                     | —                          | v0.11  | —      | [OpenID Connect][4] provider URL to enable [authentication][5]                                              |
-| OPENID_CLIENT_TRUST_STORE               | —                          | v0.26  | —      | A PKCS #12 trust store containing CA certificates needed for the [OpenID Connect][4] provider.              |
-| OPENID_CLIENT_TRUST_STORE_PASS          | —                          | v0.26  | —      | The password for the PKCS #12 trust store.                                                                  |
-| ENFORCE_REFERENTIAL_INTEGRITY           | true                       | v0.14  | —      | Enforce referential integrity on resource create, update and delete.                                        |
-| DB_SYNC_TIMEOUT                         | 10000                      | v0.15  | —      | Timeout in milliseconds for all reading FHIR interactions acquiring the newest database state.              |
-| DB_SEARCH_PARAM_BUNDLE                  | —                          | v0.21  | —      | Name of a custom search parameter bundle file.                                                              |
-| ENABLE_ADMIN_API                        | —                          | v0.26  | —      | Set to `true` if the optional Admin API should be enabled. Needed by the frontend.                          |
-| CQL_EXPR_CACHE_SIZE                     | —                          | v0.28  | —      | Size of the CQL expression cache in MiB. This cache is part of the JVM heap. Will be disabled if not given. |
-| CQL_EXPR_CACHE_REFRESH                  | PT24H                      | v0.28  | —      | The duration after which a Bloom filter of the CQL expression cache will be refreshed.                      |
-| CQL_EXPR_CACHE_THREADS                  | 4                          | v0.28  | —      | The maximum number of parallel Bloom filter calculations for the CQL expression cache.                      |
-| ALLOW_MULTIPLE_DELETE                   | false                      | v0.30  | —      | Allow deleting multiple resources using [Conditional Delete](../api.md#conditional-delete).                 |
+| Name                                    | Default                    | Since   | Depr ¹ | Description                                                                                                 |
+|:----------------------------------------|:---------------------------|:--------|--------|:------------------------------------------------------------------------------------------------------------|
+| PROXY_HOST                              | —                          | v0.6    | —      | REMOVED: use -Dhttp.proxyHost                                                                               |
+| PROXY_PORT                              | —                          | v0.6    | —      | REMOVED: use -Dhttp.proxyPort                                                                               |
+| PROXY_USER                              | —                          | v0.6.1  | —      | REMOVED: try [SOCKS Options][1]                                                                             |
+| PROXY_PASSWORD                          | —                          | v0.6.1  | —      | REMOVED: try [SOCKS Options][1]                                                                             |
+| CONNECTION_TIMEOUT                      | 5 s                        | v0.6.3  | —      | connection timeout for outbound HTTP requests                                                               |
+| REQUEST_TIMEOUT                         | 30 s                       | v0.6.3  | —      | REMOVED                                                                                                     |
+| TERM_SERVICE_URI                        | [http://tx.fhir.org/r4][6] | v0.6    | v0.11  | Base URI of the terminology service                                                                         |
+| BASE_URL                                | `http://localhost:8080`    | —       | —      | The URL under which Blaze is accessible by clients.                                                         |
+| CONTEXT_PATH                            | /fhir                      | v0.11   | —      | Context path under which the FHIR RESTful API will be accessible.                                           |
+| SERVER_PORT                             | 8080                       | —       | —      | The port of the main HTTP server                                                                            |
+| METRICS_SERVER_PORT                     | 8081                       | v0.6    | —      | The port of the Prometheus metrics server                                                                   |
+| LOG_LEVEL                               | info                       | v0.6    | —      | one of trace, debug, info, warn or error                                                                    |
+| JAVA_TOOL_OPTIONS                       | —                          | —       | —      | JVM options \(Docker only\)                                                                                 |
+| FHIR_OPERATION_EVALUATE_MEASURE_THREADS | number of CPUs             | v0.8    | —      | The number threads used for $evaluate-measure executions.                                                   |
+| FHIR_OPERATION_EVALUATE_MEASURE_TIMEOUT | 3600000 (1h)               | v0.19   | —      | Timeout in milliseconds for synchronous $evaluate-measure executions.                                       |
+| OPENID_PROVIDER_URL                     | —                          | v0.11   | —      | [OpenID Connect][4] provider URL to enable [authentication][5]                                              |
+| OPENID_CLIENT_TRUST_STORE               | —                          | v0.26   | —      | A PKCS #12 trust store containing CA certificates needed for the [OpenID Connect][4] provider.              |
+| OPENID_CLIENT_TRUST_STORE_PASS          | —                          | v0.26   | —      | The password for the PKCS #12 trust store.                                                                  |
+| ENFORCE_REFERENTIAL_INTEGRITY           | true                       | v0.14   | —      | Enforce referential integrity on resource create, update and delete.                                        |
+| DB_SYNC_TIMEOUT                         | 10000                      | v0.15   | —      | Timeout in milliseconds for all reading FHIR interactions acquiring the newest database state.              |
+| DB_SEARCH_PARAM_BUNDLE                  | —                          | v0.21   | —      | Name of a custom search parameter bundle file.                                                              |
+| ENABLE_ADMIN_API                        | —                          | v0.26   | —      | Set to `true` if the optional Admin API should be enabled. Needed by the frontend.                          |
+| CQL_EXPR_CACHE_SIZE                     | —                          | v0.28   | —      | Size of the CQL expression cache in MiB. This cache is part of the JVM heap. Will be disabled if not given. |
+| CQL_EXPR_CACHE_REFRESH                  | PT24H                      | v0.28   | —      | The duration after which a Bloom filter of the CQL expression cache will be refreshed.                      |
+| CQL_EXPR_CACHE_THREADS                  | 4                          | v0.28   | —      | The maximum number of parallel Bloom filter calculations for the CQL expression cache.                      |
+| ALLOW_MULTIPLE_DELETE                   | false                      | v0.30   | —      | Allow deleting multiple resources using [Conditional Delete](../api.md#conditional-delete).                 |
+| ENABLE_INTERACTION_DELETE_HISTORY       | -                          | v0.30.1 | —      | Enable the [Delete History](../api.md#delete-history) interaction.                                          |
+| ENABLE_OPERATION_PATIENT_PURGE          | -                          | v0.30.1 | —      | Enable the [Operation \$purge on Patient](../api/operation-patient-purge.md).                               |
 
 ¹ Deprecated