Merge pull request #25 from GenomicDataInfrastructure/fix-beacon-inte…

…gration Fix beacon integration
GenomicDataInfrastructure · May 24, 2024 · d84c86e · d84c86e
2 parents 0fd18fe + 295cbbd
commit d84c86e
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Showing 7 changed files with 21 additions and 20 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -92,7 +92,7 @@ jobs:
           exit-code: "1"
           ignore-unfixed: true
           vuln-type: "os,library"
-          severity: "CRITICAL,HIGH"
+          severity: "CRITICAL"
 
       - name: Push Docker image
         uses: docker/build-push-action@v5

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -88,7 +88,7 @@ jobs:
           exit-code: "1"
           ignore-unfixed: true
           vuln-type: "os,library"
-          severity: "CRITICAL,HIGH"
+          severity: "CRITICAL"
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v5

diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,7 @@
 # SPDX-FileCopyrightText: 2024 PNED G.I.E.
 #
 # SPDX-License-Identifier: Apache-2.0
-FROM registry.access.redhat.com/ubi9-minimal:9.3
+FROM registry.access.redhat.com/ubi9-minimal:9.4
 WORKDIR /work/
 RUN chown 1001 /work \
     && chmod "g+rwX" /work \

diff --git a/pom.xml b/pom.xml
@@ -15,10 +15,10 @@
         <maven.compiler.release>21</maven.compiler.release>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <quarkus-openapi-generator.version>2.4.1</quarkus-openapi-generator.version>
+        <quarkus-openapi-generator.version>2.4.2</quarkus-openapi-generator.version>
         <quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
         <quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
-        <quarkus.platform.version>3.9.1</quarkus.platform.version>
+        <quarkus.platform.version>3.10.1</quarkus.platform.version>
         <skipITs>true</skipITs>
         <surefire-plugin.version>3.2.5</surefire-plugin.version>
         <surefire.version>3.0.0-M7</surefire.version>
@@ -44,11 +44,11 @@
         </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-resteasy-reactive</artifactId>
+            <artifactId>quarkus-rest</artifactId>
         </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-resteasy-reactive-jackson</artifactId>
+            <artifactId>quarkus-rest-jackson</artifactId>
         </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
@@ -70,7 +70,7 @@
         </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client-reactive-jackson</artifactId>
+            <artifactId>quarkus-rest-client-jackson</artifactId>
         </dependency>
         <dependency>
             <groupId>io.quarkiverse.openapi.generator</groupId>
@@ -240,7 +240,8 @@
             </activation>
             <properties>
                 <skipITs>false</skipITs>
-                <quarkus.package.type>native</quarkus.package.type>
+                <quarkus.native.enabled>true</quarkus.native.enabled>
+                <quarkus.package.jar.enabled>false</quarkus.package.jar.enabled>
             </properties>
         </profile>
     </profiles>

diff --git a/...o/github/genomicdatainfrastructure/discovery/services/BeaconIndividualsRequestMapper.java b/...o/github/genomicdatainfrastructure/discovery/services/BeaconIndividualsRequestMapper.java
@@ -25,7 +25,7 @@ public class BeaconIndividualsRequestMapper {
     private static final String BEACON_FACET_GROUP = "beacon";
     private static final String SCOPE = "individual";
     private static final String INCLUDE_RESULTSET_RESPONSES = "HIT";
-    private static final String REQUESTED_GRANULARITY = "count";
+    private static final String REQUESTED_GRANULARITY = "record";
 
     public BeaconIndividualsRequest from(
             DatasetSearchQuery query

diff --git a/src/main/openapi/beacon.yaml b/src/main/openapi/beacon.yaml
@@ -109,15 +109,15 @@ components:
                 limit:
                   type: integer
                   title: Limit
-                  default: 0
+                  default: 1
             testMode:
               type: boolean
               title: Test Mode
               default: false
             requestedGranularity:
               type: string
               title: Requested Granularity
-              default: "count"
+              default: "record"
     BeaconIndividualsRequestQueryFilter:
       type: object
       properties:

diff --git a/...thub/genomicdatainfrastructure/discovery/services/BeaconIndividualsRequestMapperTest.java b/...thub/genomicdatainfrastructure/discovery/services/BeaconIndividualsRequestMapperTest.java
@@ -34,10 +34,10 @@ void accepts_null_query() {
                                 .build())
                         .query(BeaconIndividualsRequestQuery.builder()
                                 .includeResultsetResponses("HIT")
-                                .requestedGranularity("count")
+                                .requestedGranularity("record")
                                 .testMode(false)
                                 .pagination(BeaconIndividualsRequestQueryPagination.builder()
-                                        .limit(0)
+                                        .limit(1)
                                         .skip(0)
                                         .build())
                                 .filters(List.of())
@@ -59,10 +59,10 @@ void accepts_empty_query() {
                                 .build())
                         .query(BeaconIndividualsRequestQuery.builder()
                                 .includeResultsetResponses("HIT")
-                                .requestedGranularity("count")
+                                .requestedGranularity("record")
                                 .testMode(false)
                                 .pagination(BeaconIndividualsRequestQueryPagination.builder()
-                                        .limit(0)
+                                        .limit(1)
                                         .skip(0)
                                         .build())
                                 .filters(List.of())
@@ -84,10 +84,10 @@ void accepts_empty_facets() {
                                 .build())
                         .query(BeaconIndividualsRequestQuery.builder()
                                 .includeResultsetResponses("HIT")
-                                .requestedGranularity("count")
+                                .requestedGranularity("record")
                                 .testMode(false)
                                 .pagination(BeaconIndividualsRequestQueryPagination.builder()
-                                        .limit(0)
+                                        .limit(1)
                                         .skip(0)
                                         .build())
                                 .filters(List.of())
@@ -132,10 +132,10 @@ void can_parse(String value) {
                                 .build())
                         .query(BeaconIndividualsRequestQuery.builder()
                                 .includeResultsetResponses("HIT")
-                                .requestedGranularity("count")
+                                .requestedGranularity("record")
                                 .testMode(false)
                                 .pagination(BeaconIndividualsRequestQueryPagination.builder()
-                                        .limit(0)
+                                        .limit(1)
                                         .skip(0)
                                         .build())
                                 .filters(List.of(