Merge pull request #163 from GenomicDataInfrastructure/main

chore: promote main changes

.github/workflows/main.yml

@@ -85,7 +85,7 @@ jobs:
           load: true
 
       - name: Run Trivy vulnerability scanner
-        uses: aquasecurity/trivy-action@0.28.0
+        uses: aquasecurity/trivy-action@0.29.0
         with:
           image-ref: "${{ steps.tag.outputs.last_tag }}"
           format: "table"

.github/workflows/release.yml

@@ -81,7 +81,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
 
       - name: Run Trivy vulnerability scanner
-        uses: aquasecurity/trivy-action@0.28.0
+        uses: aquasecurity/trivy-action@0.29.0
         with:
           image-ref: "${{ steps.tag.outputs.last_tag }}"
           format: "table"

.github/workflows/test.yml

@@ -29,4 +29,4 @@ jobs:
       contents: read
     steps:
       - uses: actions/checkout@v4
-      - uses: fsfe/reuse-action@v4
+      - uses: fsfe/reuse-action@v5

.gitignore

@@ -46,4 +46,5 @@ nb-configuration.xml
 # Plugin directory
 /.quarkus/cli/plugins/
 __pycache__/
-venv/
+venv/
+infra/config/.env.secrets

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:9.4-1227.1726694542
+FROM registry.access.redhat.com/ubi9-minimal:9.5-1731604394
 WORKDIR /work/
 RUN chown 1001 /work \
     && chmod "g+rwX" /work \

_http/beacon.http

@@ -2,28 +2,93 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+
+## Ontology
+POST https://beacon-network-backend-demo.ega-archive.org/beacon-network/v2.0.0/individuals
+Content-Type: application/json
+
+{
+  "meta": {
+    "apiVersion": "2.0"
+  },
+  "query": {
+    "filters": [
+      {
+        "id": "ICD10:J40",
+        "scope": "individual"
+      }
+    ],
+    "requestParameters": [],
+    "includeResultsetResponses": "HIT",
+    "pagination": {
+      "skip": 0,
+      "limit": 1
+    },
+    "testMode": false,
+    "requestedGranularity": "record"
+  }
+}
+
+
+### Alphanumeric
+POST https://beacon-network-backend-demo.ega-archive.org/beacon-network/v2.0.0/individuals
+Content-Type: application/json
+
+{
+    "meta": {
+        "apiVersion": "2.0"
+    },
+    "query": {
+        "filters": [
+            {
+                "id": "PATO:0000011",
+                "operator": ">",
+                "value": "P30Y",
+                "scope": "individual"
+            }
+        ],
+        "requestParameters": [],
+        "includeResultsetResponses": "HIT",
+        "pagination": {
+            "skip": 0,
+            "limit": 1
+        },
+        "testMode": false,
+        "requestedGranularity": "record"
+    }
+}
+
+
+### Variants
 POST https://beacon-network-backend-demo.ega-archive.org/beacon-network/v2.0.0/individuals
 Content-Type: application/json
 
 {
-   "meta":{
-      "apiVersion":"2.0"
-   },
-   "query":{
-      "filters":[
-         {
-            "id":"UBERON:0005352",
-            "scope": "individual"
-         }
-      ],
-      "includeResultsetResponses":"HIT",
-      "pagination":{
-         "skip":0,
-         "limit":0
-      },
-      "testMode":false,
-      "requestedGranularity":"count"
-   }
+  "$schema":"beaconRequestBody.json",
+  "meta": {
+    "apiVersion": "2.0",
+    "requestedSchemas": [
+      {
+        "entityType": "genomicVariation",
+        "schema:": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json"
+      }
+    ]
+  },
+  "query": {
+    "requestParameters": {
+      "g_variant": {
+        "referenceName": "NC_000017.11",
+        "start": [7577120],
+        "referenceBases": "G",
+        "alternateBases": "A"
+      }
+    }
+  },
+  "requestedGranularity": "record",
+  "pagination": {
+    "skip": 0,
+    "limit": 10
+  }
 }
 
 ###

infra/README.md

@@ -0,0 +1,18 @@
+<!--
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+## To Run the application locally 
+
+* Create a new file named .env.secrets in infra/config by copying .env.secrets.template and updating the secret values
+* To build and start the docker image using your local changes Run the script
+
+  ```bash
+  ./start.sh
+    ```
+* To stop the application run the below script
+
+  ```bash
+  ./stop.sh
+  ```

infra/config/.env

@@ -0,0 +1,15 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+# Common Quarkus
+QUARKUS_OIDC_AUTH_SERVER_URL=https://id.portal.dev.gdi.lu/realms/gdi
+QUARKUS_OIDC_CLIENT_ID=gdi
+QUARKUS_LOG_LEVEL=DEBUG
+QUARKUS_OTEL_METRICS_ENABLED=false
+
+
+# Dataset Discovery Service
+QUARKUS_REST_CLIENT_CKAN_YAML_URL=https://catalogue.portal.dev.gdi.lu/
+QUARKUS_REST_CLIENT_BEACON_YAML_URL=https://beacon-network-backend-demo.ega-archive.org/beacon-network
+QUARKUS_REST_CLIENT_KEYCLOAK_YAML_URL=https://id.portal.dev.gdi.lu/realms/gdi
+QUARKUS_REST_CLIENT_KEYCLOAK_YAML_BEACON_IDP_ALIAS=LSAAI

infra/config/.env.secrets.template

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+QUARKUS_OIDC_CREDENTIALS_SECRET= if you do not have one ask your colleagues to share this with you

infra/docker-compose.yml

@@ -0,0 +1,18 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+services:
+  dataset-discovery-service:
+    container_name: dds
+    image: local/dds:latest
+    build:
+      context: ../
+    restart: unless-stopped
+    ports:
+      - "8080:8080"
+    env_file:
+      - ./config/.env
+      - ./config/.env.secrets
+    healthcheck:
+      test: ["CMD", "curl", "-o", "/dev/null", "http://localhost:8080/q/health"]

infra/start.sh

@@ -0,0 +1,24 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+#!/bin/bash
+
+cd ../
+
+# Run Maven build
+echo "Building the application ..."
+
+if ! mvn clean package -Dnative -Dquarkus.native.container-build=true; then
+    echo "Maven build failed. Please check the output for errors."
+    exit 1
+fi
+
+echo "Maven build completed successfully."
+
+echo "Building application docker image"
+docker build -t local/dds .
+
+echo "Docker image build completed successfully."
+
+echo "Starting application"
+docker-compose -f ./infra/docker-compose.yml up

infra/stop.sh

@@ -0,0 +1,6 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+#!/bin/bash
+
+docker-compose down

pom.xml

@@ -11,18 +11,19 @@
         <assertj.version>3.26.3</assertj.version>
         <checkstyle-maven-plugin.version>3.3.1</checkstyle-maven-plugin.version>
         <compiler-plugin.version>3.13.0</compiler-plugin.version>
-        <lombok.version>1.18.34</lombok.version>
+        <lombok.version>1.18.36</lombok.version>
         <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>2.5.0</quarkus-openapi-generator.version>
+        <quarkus-openapi-generator.version>2.6.0-lts</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>3.16.1</quarkus.platform.version>
+        <quarkus.platform.version>3.17.2</quarkus.platform.version>
         <skipITs>true</skipITs>
         <surefire.version>3.5.2</surefire.version>
         <quarkus-wiremock.version>1.4.0</quarkus-wiremock.version>
         <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
+        <mapstruct.version>1.5.5.Final</mapstruct.version>
     </properties>
     <dependencyManagement>
         <dependencies>
@@ -138,6 +139,17 @@
             <artifactId>quarkus-jacoco</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.mapstruct</groupId>
+            <artifactId>mapstruct</artifactId>
+            <version>${mapstruct.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.mapstruct</groupId>
+            <artifactId>mapstruct-processor</artifactId>
+            <version>${mapstruct.version}</version>
+            <scope>provided</scope>
+        </dependency>
     </dependencies>
     <build>
         <plugins>
@@ -172,6 +184,7 @@
                 <configuration>
                     <compilerArgs>
                         <arg>-parameters</arg>
+                        <arg>-Amapstruct.unmappedTargetPolicy=ERROR</arg>
                     </compilerArgs>
                 </configuration>
             </plugin>

src/main/java/io/github/genomicdatainfrastructure/discovery/datasets/infrastructure/beacon/persistence/BeaconDatasetIdsCollector.java

@@ -23,6 +23,7 @@
 
 import static java.util.Optional.ofNullable;
 import static java.util.stream.Collectors.toMap;
+import static org.apache.commons.lang3.ObjectUtils.isEmpty;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 @ApplicationScoped
@@ -47,7 +48,8 @@ public Map<String, Integer> collect(DatasetSearchQuery query, String accessToken
 
         var beaconQuery = BeaconIndividualsRequestMapper.from(query);
 
-        if (beaconAuthorization == null || beaconQuery.getQuery().getFilters().isEmpty()) {
+        if (beaconAuthorization == null || (isEmpty(beaconQuery.getQuery().getFilters()) &&
+                isEmpty(beaconQuery.getQuery().getRequestParameters()))) {
             return null;
         }