Merge pull request #16 from ts4nfdi/feature/add-ontoportal-api-key-en…

…v-var Feature: Add OntoPortal APIKEY env variable
ts4nfdi · Jul 24, 2024 · 89f41f7 · 89f41f7
2 parents cdb0ad6 + 2a50677
commit 89f41f7
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Showing 5 changed files with 131 additions and 53 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -1,80 +1,93 @@
 name: Continuous Integration
- 
+
 on:
   push:
-    branches: [ "main" ]
-    tags: [ "*" ]
+    branches:
+      - "main"
+    tags:
+      - "*"
+
 env:
   KUBECONFIG: .kube/config
   KUBECONFIG_FILE: ${{ secrets.KUBECONFIG }}
+
 jobs:
   build:
     name: "Build Image"
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
+
       - id: generate-image-tag
         name: Generate Image Tag
-        env:
-          ref_name: "${{ github.ref_name }}"
-          head_ref: "${{ github.head_ref }}"
         run: |
-          head_ref="${head_ref/\//-}"
-          ref_name="${head_ref:-${ref_name/main/latest}}"
-          echo "::set-output name=imageTag::${ref_name#v}"
+          head_ref="${GITHUB_HEAD_REF//\//-}"
+          ref_name="${head_ref:-${GITHUB_REF_NAME/main/latest}}"
+          echo "imageTag=${ref_name#v}" >> $GITHUB_ENV
+
       - name: Login to Docker Hub
         uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
-        
+
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          distribution: 'temurin' 
+          distribution: 'temurin'
           java-version: '11'
 
       - name: Build with Maven
         run: mvn clean install
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
+
       - name: Build and push
         uses: docker/build-push-action@v5
         with:
           context: ./
           file: ./Dockerfile
           push: true
           tags: |
-            ghcr.io/${{ github.repository }}:${{ steps.generate-image-tag.outputs.imageTag }}
+            ghcr.io/${{ github.repository }}:${{ env.imageTag }}
             ghcr.io/${{ github.repository }}:${{ github.event.pull_request.head.sha || github.sha }}
+
   deploy_main:
-      needs: build
-      if: github.ref == 'refs/heads/main'
-      runs-on: ubuntu-latest
-      steps:
+    needs: build
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
       - id: generate-image-tag
         name: Generate Image Tag
-        env:
-          ref_name: "${{ github.ref_name }}"
-          head_ref: "${{ github.head_ref }}"
         run: |
-          head_ref="${head_ref/\//-}"
-          ref_name="${head_ref:-${ref_name/main/latest}}"
-          echo "::set-output name=imageTag::${ref_name#v}"
+          head_ref="${GITHUB_HEAD_REF//\//-}"
+          ref_name="${head_ref:-${GITHUB_REF_NAME/main/latest}}"
+          echo "imageTag=${ref_name#v}" >> $GITHUB_ENV
+
       - uses: actions/checkout@v2
-      - run: |
+
+      - name: Set up Kubernetes config
+        run: |
           mkdir -p .kube
-          echo "${{ env.KUBECONFIG_FILE }}" > $KUBECONFIG
-      - uses: stefanprodan/kube-tools@v1
+          echo "${{ secrets.KUBECONFIG }}" > $KUBECONFIG
+
+      - name: Create Kubernetes secret for ONTOPORTAL_APIKEY
+        run: |
+          kubectl create secret generic ontoportal-secret \
+            --from-literal=ONTOPORTAL_APIKEY=${{ secrets.ONTOPORTAL_APIKEY }} \
+            --dry-run=client -o yaml | kubectl apply -f -
+
+      - name: Deploy to Kubernetes
+        uses: stefanprodan/kube-tools@v1
         with:
           helmv3: 3.12.0
           command: |
             kubectl get nodes
             helmv3 repo add api-gateway-deployment https://ts4nfdi.github.io/api-gateway-deployment/
             helmv3 repo update
             helmv3 upgrade ts4nfdi \
-            --install \
-            api-gateway-deployment/api-gateway
+              --install \
+              api-gateway-deployment/api-gateway
diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -8,6 +8,8 @@ services:
     container_name: api-gateway
     ports:
       - "8080:8080"
+    environment:
+      ONTOPORTAL_APIKEY: "put here APIKEY"
     restart: always
     networks:
       - api-gateway

diff --git a/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java b/src/main/java/org/semantics/apigateway/service/ConfigurationLoader.java
@@ -0,0 +1,74 @@
+package org.semantics.apigateway.service;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lombok.Getter;
+import org.semantics.apigateway.config.DatabaseConfig;
+import org.semantics.apigateway.config.OntologyConfig;
+import org.semantics.apigateway.model.DynTransformResponse;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.ResourceLoader;
+import org.springframework.stereotype.Service;
+import org.springframework.util.StreamUtils;
+import org.springframework.web.client.RestTemplate;
+
+import javax.annotation.PostConstruct;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+@Service
+@Getter
+public class ConfigurationLoader {
+
+    @Autowired
+    private ConfigurableEnvironment environment;
+
+    @Autowired
+    private ResourceLoader resourceLoader;
+
+    private static final Logger logger = LoggerFactory.getLogger(DynSearchService.class);
+    private List<OntologyConfig> ontologyConfigs;
+    private Map<String, Map<String, String>> responseMappings;
+
+    // Method invoked after on server start, loads database configurations and replace environment variables
+    @PostConstruct
+    public void loadDbConfigs() throws IOException {
+        Resource resource = resourceLoader.getResource("classpath:response-config.json");
+        String jsonContent = StreamUtils.copyToString(resource.getInputStream(), StandardCharsets.UTF_8);
+
+        for (Map.Entry<String, Object> property : environment.getSystemEnvironment().entrySet()) {
+            String key = property.getKey();
+            String value = (String) property.getValue();
+            jsonContent = jsonContent.replace("${" + key + "}", value);
+        }
+
+        ObjectMapper objectMapper = new ObjectMapper();
+        DatabaseConfig dbConfig = objectMapper.readValue(jsonContent, DatabaseConfig.class);
+        this.ontologyConfigs = dbConfig.getDatabases();
+        this.responseMappings = loadResponseMappings();
+        ontologyConfigs.forEach(config -> logger.info("Loaded config: {}", config));
+    }
+
+    // Loads response mappings from a json configuration file
+    private Map<String, Map<String, String>> loadResponseMappings() throws IOException {
+        InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream("response-mappings.json");
+        if (inputStream != null) {
+            ObjectMapper objectMapper = new ObjectMapper();
+            Map<String, Map<String, String>> mappings = objectMapper.readValue(inputStream, new TypeReference<Map<String, Map<String, String>>>() {
+            });
+            if (mappings != null) {
+                return mappings;
+            }
+        }
+        return Collections.emptyMap();
+    }
+
+}
diff --git a/src/main/java/org/semantics/apigateway/service/DynSearchService.java b/src/main/java/org/semantics/apigateway/service/DynSearchService.java
@@ -10,17 +10,25 @@
 import org.semantics.apigateway.model.JsonLdTransform;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.Environment;
+import org.springframework.core.env.MutablePropertySources;
+import org.springframework.core.env.PropertySource;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.core.io.Resource;
+import org.springframework.core.io.ResourceLoader;
 import org.springframework.http.ResponseEntity;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Service;
+import org.springframework.util.StreamUtils;
 import org.springframework.web.client.RestTemplate;
 
 import javax.annotation.PostConstruct;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -32,38 +40,19 @@
 @Service
 public class DynSearchService {
 
-    // Resource path to the JSON configuration file for database configurations
-    @Value("classpath:response-config.json")
-    private Resource dbConfigResource;
+    private ConfigurationLoader configurationLoader;
     private static final Logger logger = LoggerFactory.getLogger(DynSearchService.class);
     private final RestTemplate restTemplate = new RestTemplate();
     private final DynTransformResponse dynTransformResponse = new DynTransformResponse();
     private List<OntologyConfig> ontologyConfigs;
     private Map<String, Map<String, String>> responseMappings;
 
-    // Method invoked after the bean’s properties have been set, loads database configurations
-    @PostConstruct
-    public void loadDbConfigs() throws IOException {
-     ObjectMapper objectMapper = new ObjectMapper();
-        try (InputStream in = dbConfigResource.getInputStream()) {
-            DatabaseConfig dbConfig = objectMapper.readValue(in, DatabaseConfig.class);
-            this.ontologyConfigs = dbConfig.getDatabases();
-            this.responseMappings = loadResponseMappings();
-            ontologyConfigs.forEach(config -> logger.info("Loaded config: {}", config));
-        }
-    }
 
-    // Loads response mappings from a json configuration file
-    private Map<String, Map<String, String>> loadResponseMappings() throws IOException {
-        InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream("response-mappings.json");
-        if (inputStream != null) {
-            ObjectMapper objectMapper = new ObjectMapper();
-            Map<String, Map<String, String>> mappings = objectMapper.readValue(inputStream, new TypeReference<Map<String, Map<String, String>>>(){});
-            if (mappings != null) {
-                return mappings;
-            }
-        }
-        return Collections.emptyMap();
+    @Autowired
+    public DynSearchService(ConfigurationLoader configurationLoader) {
+        this.configurationLoader = configurationLoader;
+        this.ontologyConfigs = configurationLoader.getOntologyConfigs();
+        this.responseMappings = configurationLoader.getResponseMappings();
     }
 
     // Constructs the URL for the API call based on the query and configuration

diff --git a/src/main/resources/response-config.json b/src/main/resources/response-config.json
@@ -3,7 +3,7 @@
     {
       "database": "ontoportal",
       "url": "https://data.biodivportal.gfbio.dev/search?q=%s&apikey=%s",
-      "apiKey": "xxx",
+      "apiKey": "${ONTOPORTAL_APIKEY}",
       "responseMapping": {
         "nestedJson": "collection",
         "label": "prefLabel",