feat: support for SQL database connection settings

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

@@ -1,7 +1,10 @@
 package eu.bbmri_eric.quality.agent.dataquality;
 
+import eu.bbmri_eric.quality.agent.dataquality.dto.DatabaseHealthDTO;
+import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
 import org.json.JSONObject;
 
+/** Provides connectivity to a database on which the Data Quality Checks should be executed. */
 public interface DataStore {
   /**
    * Retrieves an entity of the specified type and ID from the data store.
@@ -14,4 +17,20 @@ public interface DataStore {
   JSONObject getEntity(String entityType, String id) throws Exception;
 
   JSONObject checkHealth() throws Exception;
+
+  /**
+   * Executes a query against the connected database.
+   *
+   * @param query the query string to execute. e.g., SQL or CQL
+   * @return the result of the query execution as a {@link ResultDTO}
+   */
+  ResultDTO executeQuery(String query);
+
+  /**
+   * Checks the health of the database connection.
+   *
+   * @return a {@link eu.bbmri_eric.quality.agent.dataquality.dto.DatabaseHealthDTO} containing the
+   *     current health status and metrics of the database connection
+   */
+  DatabaseHealthDTO checkHealthV2();
 }

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

@@ -0,0 +1,11 @@
+package eu.bbmri_eric.quality.agent.dataquality;
+
+/** Factory for selecting the active {@link DataStore} based on current settings. */
+public interface DataStoreFactory {
+  /**
+   * Resolves the data store that should be used based on current settings.
+   *
+   * @return the resolved {@link DataStore}
+   */
+  DataStore resolveDataStore();
+}

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/FHIRStore.java → agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/FHIRServer.java

@@ -9,7 +9,7 @@
  * FHIR resources such as Libraries and Measures. It provides methods to interact with and query the
  * FHIR backend.
  */
-public interface FHIRStore {
+public interface FHIRServer extends DataStore {
 
   /**
    * Returns a base JSON template for creating a FHIR Library resource.

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

@@ -1,22 +1,22 @@
 package eu.bbmri_eric.quality.agent.dataquality.domain;
 
-import eu.bbmri_eric.quality.agent.dataquality.FHIRStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStore;
 import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
 
 /**
  * Represents a singular executable query that determines a specific aspect of data quality.
  * Implementations of this interface encapsulate the logic for evaluating data quality against a
- * given FHIR data store.
+ * given data store.
  */
 public interface DataQualityCheck {
 
   /**
-   * Executes the data quality check against the specified FHIR store.
+   * Executes the data quality check against the specified data store.
    *
-   * @param fhirStore the FHIR store against which the data quality check should be executed
+   * @param dataStore the data store against which the data quality check should be executed
    * @return the result of the data quality check
    */
-  ResultDTO execute(FHIRStore fhirStore);
+  ResultDTO execute(DataStore dataStore);
 
   /**
    * Returns the human-readable name of the data quality check.

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/domain/QualityCheck.java

@@ -1,8 +1,6 @@
 package eu.bbmri_eric.quality.agent.dataquality.domain;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.bbmri_eric.quality.agent.dataquality.FHIRStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStore;
 import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
 import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
@@ -13,12 +11,8 @@
 import jakarta.persistence.Id;
 import jakarta.validation.constraints.NotBlank;
 import jakarta.validation.constraints.NotNull;
-import java.util.Base64;
-import java.util.HashSet;
-import java.util.Set;
 import lombok.Getter;
 import lombok.Setter;
-import org.json.JSONObject;
 
 /** A data quality check utilizing the Hl7 Clinical Quality Language queries for evaluation. */
 @Entity(name = "quality_check")
@@ -59,42 +53,13 @@ public QualityCheck(String name, String description, String query) {
     this.query = query;
   }
 
-  private static final ObjectMapper mapper = new ObjectMapper();
-
   @Override
-  public ResultDTO execute(FHIRStore fhirStore) {
+  public ResultDTO execute(DataStore dataStore) {
     try {
-      String cqlData = Base64.getEncoder().encodeToString(query.getBytes());
-      String libraryUri = java.util.UUID.randomUUID().toString().toLowerCase();
-      String measureUri = java.util.UUID.randomUUID().toString().toLowerCase();
-      JSONObject libraryResource = fhirStore.createLibrary(libraryUri, cqlData);
-      fhirStore.postResource("Library", libraryResource);
-      JSONObject measureResource = fhirStore.createMeasure(measureUri, libraryUri, "Patient");
-      JSONObject measureResponse = fhirStore.postResource("Measure", measureResource);
-      String measureId = measureResponse.getString("id");
-      JSONObject measureReport = fhirStore.evaluateMeasureList(measureId);
-      JsonNode mr = mapper.readTree(measureReport.toString());
-
-      int count = mr.at("/group/0/population/0/count").asInt();
-      Set<String> idSet = new HashSet<>();
-      if (count != 0) {
-        String listRef = mr.at("/group/0/population/0/subjectResults/reference").asText(null);
-        if (listRef != null && listRef.startsWith("List/")) {
-          String listId = listRef.substring("List/".length());
-
-          JSONObject listResource = fhirStore.getPatientList(listId);
-          JsonNode lr = mapper.readTree(listResource.toString());
-
-          for (JsonNode entry : lr.withArray("entry")) {
-            String ref = entry.at("/item/reference").asText(null);
-            if (ref != null && ref.startsWith("Patient/")) {
-              idSet.add(ref.substring("Patient/".length()));
-            }
-          }
-        }
-      }
-
-      return new ResultDTO(count, "Patient", idSet);
+      ResultDTO result = dataStore.executeQuery(query);
+      return result != null
+          ? result
+          : new ResultDTO("No result returned from data store execution.");
     } catch (Exception | NoSuchMethodError e) {
       return new ResultDTO(e.getMessage());
     }

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/domain/QualityCheckType.java

@@ -6,5 +6,6 @@ public enum QualityCheckType {
   CQL,
 
   /** Java-based built-in check implementation. */
-  JAVA
+  JAVA,
+  SQL
 }

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/dto/DBStatus.java

@@ -0,0 +1,6 @@
+package eu.bbmri_eric.quality.agent.dataquality.dto;
+
+public enum DBStatus {
+  UP,
+  DOWN
+}

agent/backend/src/main/java/eu/bbmri_eric/quality/agent/dataquality/dto/DatabaseHealthDTO.java

@@ -0,0 +1,33 @@
+package eu.bbmri_eric.quality.agent.dataquality.dto;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+import lombok.AccessLevel;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Setter
+@NoArgsConstructor(access = AccessLevel.PROTECTED)
+@AllArgsConstructor
+@Schema(name = "Database Health", description = "Health status information for the database")
+public class DatabaseHealthDTO {
+  @Schema(
+      description = "Overall health status of the database",
+      example = "UP",
+      requiredMode = Schema.RequiredMode.REQUIRED)
+  public DBStatus status;
+
+  @Schema(
+      description = "Error message if the database is unhealthy",
+      example = "Connection refused",
+      requiredMode = Schema.RequiredMode.NOT_REQUIRED)
+  public String error;
+
+  @Schema(
+      description = "Additional details about the health status",
+      example = "Database connection pool exhausted",
+      requiredMode = Schema.RequiredMode.NOT_REQUIRED)
+  public String details;
+}

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

@@ -1,6 +1,7 @@
 package eu.bbmri_eric.quality.agent.dataquality.impl;
 
-import eu.bbmri_eric.quality.agent.dataquality.FHIRStore;
+import eu.bbmri_eric.quality.agent.dataquality.DataStore;
+import eu.bbmri_eric.quality.agent.dataquality.FHIRServer;
 import eu.bbmri_eric.quality.agent.dataquality.domain.DataQualityCheck;
 import eu.bbmri_eric.quality.agent.dataquality.domain.QualityCheck;
 import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
@@ -33,7 +34,10 @@ class DuplicateIdentifierCheck implements DataQualityCheck {
   }
 
   @Override
-  public ResultDTO execute(FHIRStore fhirStore) {
+  public ResultDTO execute(DataStore dataStore) {
+    if (!(dataStore instanceof FHIRServer fhirStore)) {
+      return new ResultDTO("FHIR data store required for " + getName());
+    }
     try {
       List<Resource> patients = fhirStore.fetchAllResources("Patient", List.of("id", "identifier"));
       Map<String, List<String>> identifierMap = new HashMap<>();

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

@@ -1,6 +1,8 @@
 package eu.bbmri_eric.quality.agent.dataquality.impl;
 
-import eu.bbmri_eric.quality.agent.dataquality.FHIRStore;
+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;
 import lombok.extern.slf4j.Slf4j;
@@ -10,16 +12,22 @@
 @Component
 class EntityCountStep implements ReportPipelineStep {
 
-  private final FHIRStore fhirStore;
+  private final DataStoreFactory dataStoreFactory;
 
-  EntityCountStep(FHIRStore 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/FhirCqlQueryExecutor.java

@@ -0,0 +1,54 @@
+package eu.bbmri_eric.quality.agent.dataquality.impl;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.bbmri_eric.quality.agent.dataquality.FHIRServer;
+import eu.bbmri_eric.quality.agent.dataquality.dto.ResultDTO;
+import java.util.Base64;
+import java.util.HashSet;
+import java.util.Set;
+import org.json.JSONObject;
+
+public final class FhirCqlQueryExecutor {
+  private static final ObjectMapper mapper = new ObjectMapper();
+
+  private FhirCqlQueryExecutor() {}
+
+  public static ResultDTO execute(FHIRServer fhirStore, String query) {
+    try {
+      String cqlData = Base64.getEncoder().encodeToString(query.getBytes());
+      String libraryUri = java.util.UUID.randomUUID().toString().toLowerCase();
+      String measureUri = java.util.UUID.randomUUID().toString().toLowerCase();
+      JSONObject libraryResource = fhirStore.createLibrary(libraryUri, cqlData);
+      fhirStore.postResource("Library", libraryResource);
+      JSONObject measureResource = fhirStore.createMeasure(measureUri, libraryUri, "Patient");
+      JSONObject measureResponse = fhirStore.postResource("Measure", measureResource);
+      String measureId = measureResponse.getString("id");
+      JSONObject measureReport = fhirStore.evaluateMeasureList(measureId);
+      JsonNode mr = mapper.readTree(measureReport.toString());
+
+      int count = mr.at("/group/0/population/0/count").asInt();
+      Set<String> idSet = new HashSet<>();
+      if (count != 0) {
+        String listRef = mr.at("/group/0/population/0/subjectResults/reference").asText(null);
+        if (listRef != null && listRef.startsWith("List/")) {
+          String listId = listRef.substring("List/".length());
+
+          JSONObject listResource = fhirStore.getPatientList(listId);
+          JsonNode lr = mapper.readTree(listResource.toString());
+
+          for (JsonNode entry : lr.withArray("entry")) {
+            String ref = entry.at("/item/reference").asText(null);
+            if (ref != null && ref.startsWith("Patient/")) {
+              idSet.add(ref.substring("Patient/".length()));
+            }
+          }
+        }
+      }
+
+      return new ResultDTO(count, "Patient", idSet);
+    } catch (Exception | NoSuchMethodError e) {
+      return new ResultDTO(e.getMessage());
+    }
+  }
+}