feat(agent): add support for SQL database settings

Author: RadovanTomik

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/DataStoreFactory.java

@@ -9,4 +9,3 @@ public interface DataStoreFactory {
    */
   DataStore resolveDataStore();
 }
-

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/config/DataStoreConfiguration.java

@@ -1,6 +1,7 @@
 package eu.bbmri_eric.quality.agent.dataquality.controller;
 
 import eu.bbmri_eric.quality.agent.dataquality.DataStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStoreFactory;
 import java.util.NoSuchElementException;
 import org.json.JSONObject;
 import org.springframework.http.MediaType;
@@ -13,15 +14,16 @@
 @RestController
 @RequestMapping("/api/entities")
 class EntityController {
-  private final DataStore dataStore;
+  private final DataStoreFactory dataStoreFactory;
 
-  EntityController(DataStore dataStore) {
-    this.dataStore = dataStore;
+  EntityController(DataStoreFactory dataStoreFactory) {
+    this.dataStoreFactory = dataStoreFactory;
   }
 
   @GetMapping("{entityType}/{id}")
   public ResponseEntity<String> getEntity(
       @PathVariable String entityType, @PathVariable String id) {
+    DataStore dataStore = dataStoreFactory.resolveDataStore();
     try {
       JSONObject response = dataStore.getEntity(entityType, id);
       if (response == null) {
@@ -39,6 +41,7 @@ public ResponseEntity<String> getEntity(
 
   @GetMapping("health")
   public ResponseEntity<String> checkHealth() {
+    DataStore dataStore = dataStoreFactory.resolveDataStore();
     try {
       JSONObject healthResult = dataStore.checkHealth();
 

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/controller/EntityController.java

@@ -38,9 +38,9 @@
 import org.springframework.http.HttpMethod;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.client.HttpComponentsClientHttpRequestFactory;
-import org.springframework.stereotype.Component;
 import org.springframework.web.client.HttpClientErrorException;
 import org.springframework.web.client.RestTemplate;
+
 class BlazeFHIRStore implements FHIRServer {
   private static final Logger log = LoggerFactory.getLogger(BlazeFHIRStore.class);
   private final RestTemplateBuilder restTemplateBuilder;

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/impl/BlazeFHIRStore.java

@@ -5,8 +5,10 @@
 import eu.bbmri_eric.quality.agent.settings.DatabaseType;
 import eu.bbmri_eric.quality.agent.settings.SettingsService;
 import eu.bbmri_eric.quality.agent.settings.dto.SettingsDTO;
+import eu.bbmri_eric.quality.agent.settings.event.SettingsUpdatedEvent;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.boot.web.client.RestTemplateBuilder;
+import org.springframework.context.event.EventListener;
 import org.springframework.stereotype.Component;
 
 @Slf4j
@@ -15,6 +17,7 @@ class DataStoreFactoryImpl implements DataStoreFactory {
   private final SettingsService settingsService;
   private final BlazeFHIRStore fhirDataStore;
   private final SqlDataStore sqlDataStore;
+  private volatile DataStore currentDataStore;
 
   DataStoreFactoryImpl(SettingsService settingsService, RestTemplateBuilder restTemplateBuilder) {
     this.settingsService = settingsService;
@@ -24,7 +27,23 @@ class DataStoreFactoryImpl implements DataStoreFactory {
 
   @Override
   public DataStore resolveDataStore() {
-    SettingsDTO settings = settingsService.getSettings();
+    DataStore cached = currentDataStore;
+    if (cached != null) {
+      return cached;
+    }
+    return resolveFromSettings(settingsService.getSettings());
+  }
+
+  @EventListener
+  public void onSettingsUpdated(SettingsUpdatedEvent event) {
+    log.info("Settings updated, refreshing active data store");
+    this.currentDataStore = resolveFromSettings(event.getSettings());
+    if (event.getSettings().getDatabaseType() == DatabaseType.FHIR) {
+      fhirDataStore.onSettingsUpdated(event);
+    }
+  }
+
+  private DataStore resolveFromSettings(SettingsDTO settings) {
     DatabaseType databaseType = settings != null ? settings.getDatabaseType() : null;
     if (databaseType == null) {
       log.warn("Database type not configured, defaulting to FHIR data store.");

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/impl/DataStoreFactoryImpl.java

@@ -1,5 +1,7 @@
 package eu.bbmri_eric.quality.agent.dataquality.impl;
 
+import eu.bbmri_eric.quality.agent.dataquality.DataStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStoreFactory;
 import eu.bbmri_eric.quality.agent.dataquality.FHIRServer;
 import eu.bbmri_eric.quality.agent.dataquality.ReportPipelineStep;
 import eu.bbmri_eric.quality.agent.dataquality.domain.Report;
@@ -10,16 +12,22 @@
 @Component
 class EntityCountStep implements ReportPipelineStep {
 
-  private final FHIRServer fhirStore;
+  private final DataStoreFactory dataStoreFactory;
 
-  EntityCountStep(FHIRServer fhirStore) {
-    this.fhirStore = fhirStore;
+  EntityCountStep(DataStoreFactory dataStoreFactory) {
+    this.dataStoreFactory = dataStoreFactory;
   }
 
   @Override
   public Report execute(Report report) {
     log.info("Counting entities for report id: {}", report.getId());
 
+    DataStore dataStore = dataStoreFactory.resolveDataStore();
+    if (!(dataStore instanceof FHIRServer fhirStore)) {
+      log.info("Skipping entity count: not a FHIR data store");
+      return report;
+    }
+
     Integer patientCount = fhirStore.countResources("Patient");
     Integer sampleCount = fhirStore.countResources("Specimen");
 

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/impl/EntityCountStep.java

@@ -1,6 +1,7 @@
 package eu.bbmri_eric.quality.agent.dataquality.impl;
 
 import eu.bbmri_eric.quality.agent.dataquality.DataStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStoreFactory;
 import eu.bbmri_eric.quality.agent.dataquality.FHIRServer;
 import eu.bbmri_eric.quality.agent.dataquality.ReportPipelineStep;
 import eu.bbmri_eric.quality.agent.dataquality.domain.DataQualityCheck;
@@ -23,31 +24,35 @@
 class QualityChecksStep implements ReportPipelineStep {
 
   private final QualityCheckRepository repository;
-  private final DataStore dataStore;
+  private final DataStoreFactory dataStoreFactory;
   private final ModelMapper modelMapper;
 
   QualityChecksStep(
-      QualityCheckRepository repository, DataStore dataStore, ModelMapper modelMapper) {
+      QualityCheckRepository repository,
+      DataStoreFactory dataStoreFactory,
+      ModelMapper modelMapper) {
     this.repository = repository;
-    this.dataStore = dataStore;
+    this.dataStoreFactory = dataStoreFactory;
     this.modelMapper = modelMapper;
   }
 
   @Override
   public Report execute(Report report) {
     log.info("Running quality checks for report id: {}", report.getId());
+    DataStore dataStore = dataStoreFactory.resolveDataStore();
     List<DataQualityCheck> dataQualityChecks = compileChecksToRun(dataStore);
-    runRelevantChecks(report, dataQualityChecks);
+    runRelevantChecks(report, dataQualityChecks, dataStore);
     log.info("Completed quality checks for report id: {}", report.getId());
     return report;
   }
 
-  private void runRelevantChecks(Report report, List<DataQualityCheck> dataQualityChecks) {
+  private void runRelevantChecks(
+      Report report, List<DataQualityCheck> dataQualityChecks, DataStore dataStore) {
     for (DataQualityCheck dataQualityCheck : dataQualityChecks) {
       if (dataQualityCheck instanceof StratifiedDataQualityCheck stratifiedCheck) {
-        executeStratifiedCheck(stratifiedCheck, report);
+        executeStratifiedCheck(stratifiedCheck, report, dataStore);
       } else {
-        executeCheck(dataQualityCheck, report);
+        executeCheck(dataQualityCheck, report, dataStore);
       }
     }
   }
@@ -83,7 +88,8 @@ private Optional<DataQualityCheck> createBuiltInCheck(QualityCheck config) {
     return Optional.empty();
   }
 
-  private void executeStratifiedCheck(StratifiedDataQualityCheck check, Report report) {
+  private void executeStratifiedCheck(
+      StratifiedDataQualityCheck check, Report report, DataStore dataStore) {
     if (!(dataStore instanceof FHIRServer fhirStore)) {
       ResultDTO resultDTO = new ResultDTO("FHIR data store required for " + check.getName());
       Result result = modelMapper.map(resultDTO, Result.class);
@@ -105,7 +111,7 @@ private void executeStratifiedCheck(StratifiedDataQualityCheck check, Report rep
     }
   }
 
-  private void executeCheck(DataQualityCheck check, Report report) {
+  private void executeCheck(DataQualityCheck check, Report report, DataStore dataStore) {
     ResultDTO resultDTO = check.execute(dataStore);
     Result result = modelMapper.map(resultDTO, Result.class);
     modelMapper.map(check, result);

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/impl/QualityChecksStep.java

@@ -1,17 +1,15 @@
 package eu.bbmri_eric.quality.agent.dataquality.impl;
 
 import eu.bbmri_eric.quality.agent.dataquality.DataStore;
-import eu.bbmri_eric.quality.agent.dataquality.dto.DatabaseHealthDTO;
 import eu.bbmri_eric.quality.agent.dataquality.dto.DBStatus;
+import eu.bbmri_eric.quality.agent.dataquality.dto.DatabaseHealthDTO;
 import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
 import org.json.JSONObject;
-import org.springframework.stereotype.Component;
 
 class SqlDataStore implements DataStore {
   private static final String NOT_IMPLEMENTED_MESSAGE = "SQL data store not implemented yet.";
 
-  public SqlDataStore() {
-  }
+  public SqlDataStore() {}
 
   @Override
   public JSONObject getEntity(String entityType, String id) {
@@ -36,4 +34,3 @@ public DatabaseHealthDTO checkHealthV2() {
     return new DatabaseHealthDTO(DBStatus.DOWN, NOT_IMPLEMENTED_MESSAGE, null);
   }
 }
-

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/impl/SqlDataStore.java

@@ -4,6 +4,7 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import eu.bbmri_eric.quality.agent.dataquality.DataStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStoreFactory;
 import org.json.JSONObject;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;
@@ -14,10 +15,13 @@ class DataStoreTest {
   @Test
   void getEntity_success() throws Exception {
     DataStore mockDataStore = Mockito.mock(DataStore.class);
+    DataStoreFactory mockFactory = Mockito.mock(DataStoreFactory.class);
+    Mockito.when(mockFactory.resolveDataStore()).thenReturn(mockDataStore);
+
     JSONObject entity = new JSONObject().put("id", "123").put("type", "Patient");
     Mockito.when(mockDataStore.getEntity("Patient", "123")).thenReturn(entity);
 
-    EntityController controller = new EntityController(mockDataStore);
+    EntityController controller = new EntityController(mockFactory);
     ResponseEntity<String> response = controller.getEntity("Patient", "123");
 
     assertEquals(200, response.getStatusCodeValue());
@@ -28,10 +32,13 @@ void getEntity_success() throws Exception {
   @Test
   void getEntity_error() throws Exception {
     DataStore mockDataStore = Mockito.mock(DataStore.class);
+    DataStoreFactory mockFactory = Mockito.mock(DataStoreFactory.class);
+    Mockito.when(mockFactory.resolveDataStore()).thenReturn(mockDataStore);
+
     Mockito.when(mockDataStore.getEntity("Patient", "fail"))
         .thenThrow(new RuntimeException("Not found"));
 
-    EntityController controller = new EntityController(mockDataStore);
+    EntityController controller = new EntityController(mockFactory);
     ResponseEntity<String> response = controller.getEntity("Patient", "fail");
 
     assertEquals(500, response.getStatusCodeValue());

agent/backend/src/test/java/eu/bbmri_eric/quality/agent/dataquality/controller/DataStoreTest.java

@@ -21,14 +21,14 @@
                 : 'bi-exclamation-triangle-fill',
             ]"
           ></i>
-          <strong>FHIR® Server:</strong> {{ healthStore.healthStatus.status }}
+          <strong>{{ dataSourceLabel }}:</strong> {{ healthStore.healthStatus.status }}
           <span v-if="healthStore.healthStatus.details?.error" class="ms-2">
             - {{ healthStore.healthStatus.details.error }}</span
           >
         </span>
         <small v-if="healthStore.healthStatus.status !== 'UP'" class="mt-2 tip-text">
           <i class="bi bi-info-circle me-1"></i>
-          Tip: Check your FHIR® server connection details in
+          Tip: Check your {{ dataSourceLabel }} connection details in
           <router-link to="/settings" class="settings-link">Settings</router-link>
         </small>
       </div>
@@ -49,9 +49,16 @@
 </template>
 
 <script setup>
+  import { computed } from 'vue';
   import { useHealthStore } from '@/stores/healthStore.js';
+  import { useSettingsStore } from '@/stores/settingsStore.js';
 
   const healthStore = useHealthStore();
+  const settingsStore = useSettingsStore();
+
+  const isSql = computed(() => settingsStore.settings?.databaseType === 'SQL');
+
+  const dataSourceLabel = computed(() => (isSql.value ? 'SQL Database' : 'FHIR® Server'));
 </script>
 
 <style scoped>