EBISPOT · henrietteharmse · Jul 15, 2024 · Jul 15, 2024
diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java
@@ -21,6 +21,8 @@
 import org.apache.solr.client.solrj.response.FacetField.Count;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.stereotype.Controller;
@@ -34,6 +36,7 @@
 
 import org.springframework.web.bind.annotation.RestController;
 import uk.ac.ebi.spot.ols.repository.Validation;
+import uk.ac.ebi.spot.ols.repository.neo4j.OlsNeo4jClient;
 import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
 import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;
 import uk.ac.ebi.spot.ols.repository.transforms.RemoveLiteralDatatypesTransform;
@@ -59,6 +62,8 @@ public class V1SearchController {
     private OlsSolrClient solrClient;
 
 
+    private static final Logger logger = LoggerFactory.getLogger(V1SearchController.class);
+
     @RequestMapping(path = "/api/search", produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
     public void search(
             @RequestParam("q") String query,
@@ -81,8 +86,6 @@ public void search(
             @RequestParam(value = "lang", defaultValue = "en") String lang,
             HttpServletResponse response
     ) throws IOException, SolrServerException {
-        System.out.println("fieldList 1 = " + fieldList);
-        System.out.println("type = " + types);
 
         final SolrQuery solrQuery = new SolrQuery(); // 1
 
@@ -208,15 +211,13 @@ public void search(
 		 * Fix: End
 		 */
         solrQuery.add("wt", format);
-        System.out.println("fieldList 2 = " + fieldList);
 
-        System.out.println("solrQuery=" + solrQuery.jsonStr());
+        logger.debug("search: ()", solrQuery.toQueryString());
 
         QueryResponse qr = solrClient.dispatchSearch(solrQuery, "ols4_entities");
 
         List<Object> docs = new ArrayList<>();
         for(SolrDocument res : qr.getResults()) {
-            System.out.println("res = " + res.toString());
             String _json = (String)res.get("_json");
             if(_json == null) {
                 throw new RuntimeException("_json was null");

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java
@@ -9,6 +9,8 @@
 import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.stereotype.Controller;
@@ -17,6 +19,7 @@
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 import uk.ac.ebi.spot.ols.repository.Validation;
+import uk.ac.ebi.spot.ols.repository.neo4j.OlsNeo4jClient;
 import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
 import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;
 import uk.ac.ebi.spot.ols.repository.transforms.RemoveLiteralDatatypesTransform;
@@ -42,6 +45,8 @@ public class V1SelectController {
     @Autowired
     private OlsSolrClient solrClient;
 
+    private static final Logger logger = LoggerFactory.getLogger(V1SelectController.class);
+
     @RequestMapping(path = "/api/select", produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
     public void select(
             @RequestParam("q") String query,
@@ -118,7 +123,7 @@ public void select(
         solrQuery.addHighlightField("whitespace_edge_synonym");
         solrQuery.addHighlightField("synonym");
 
-        System.out.println("select: " + solrQuery.toQueryString());
+       logger.debug("select: ()", solrQuery.toQueryString());
 
         QueryResponse qr = solrClient.dispatchSearch(solrQuery, "ols4_entities");
 

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/neo4j/OlsNeo4jClient.java b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/neo4j/OlsNeo4jClient.java
@@ -1,11 +1,14 @@
 package uk.ac.ebi.spot.ols.repository.neo4j;
 
 import com.google.gson.JsonElement;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Component;
+import uk.ac.ebi.spot.ols.repository.solr.OlsSolrClient;
 import uk.ac.ebi.spot.ols.service.Neo4jClient;
 
 import java.util.List;
@@ -19,6 +22,8 @@ public class OlsNeo4jClient {
 	@Autowired
 	Neo4jClient neo4jClient;
 
+	private static final Logger logger = LoggerFactory.getLogger(OlsNeo4jClient.class);
+
     public Page<JsonElement> getAll(String type, Map<String,String> properties, Pageable pageable) {
 
 		String query = "MATCH (a:" + type + ")";
@@ -71,40 +76,40 @@ private String makeEdgePropsClause(Map<String,String> edgeProps) {
 
     public Page<JsonElement> traverseOutgoingEdges(String type, String id, List<String> edgeIRIs, Map<String,String> edgeProps, Pageable pageable) {
 
-	String edge = makeEdgesList(edgeIRIs, edgeProps);
+		String edge = makeEdgesList(edgeIRIs, edgeProps);
 
-	// TODO fix injection
+		// TODO fix injection
 
-	String query =
-	  "MATCH (a:" + type+ ")-[edge:" + edge + "]->(b) "
-	+ "WHERE a.id = $id " + makeEdgePropsClause(edgeProps)
-	+ "RETURN distinct b";
+		String query =
+		  "MATCH (a:" + type+ ")-[edge:" + edge + "]->(b) "
+		+ "WHERE a.id = $id " + makeEdgePropsClause(edgeProps)
+		+ "RETURN distinct b";
 
-	String countQuery =
-	  "MATCH (a:" + type + ")-[edge:" + edge + "]->(b) "
-	+ "WHERE a.id = $id " + makeEdgePropsClause(edgeProps)
-	+ "RETURN count(distinct b)";
+		String countQuery =
+		  "MATCH (a:" + type + ")-[edge:" + edge + "]->(b) "
+		+ "WHERE a.id = $id " + makeEdgePropsClause(edgeProps)
+		+ "RETURN count(distinct b)";
 
-		System.out.println(query);
+		logger.trace(query);
 
 		return neo4jClient.queryPaginated(query, "b", countQuery, parameters("type", type, "id", id), pageable);
     }
 
     public Page<JsonElement> traverseIncomingEdges(String type, String id, List<String> edgeIRIs, Map<String,String> edgeProps, Pageable pageable) {
 
-	String edge = makeEdgesList(edgeIRIs, Map.of());
+		String edge = makeEdgesList(edgeIRIs, Map.of());
 
-	String query =
-	  "MATCH (a:" + type + ")<-[edge:" + edge + "]-(b) "
-	+ "WHERE a.id = $id "
-	+ "RETURN distinct b";
+		String query =
+		  "MATCH (a:" + type + ")<-[edge:" + edge + "]-(b) "
+		+ "WHERE a.id = $id "
+		+ "RETURN distinct b";
 
-	String countQuery =
-	  "MATCH (a:" + type + ")<-[edge:" + edge + "]-(b) "
-	+ "WHERE a.id = $id "
-	+ "RETURN count(distinct b)";
+		String countQuery =
+		  "MATCH (a:" + type + ")<-[edge:" + edge + "]-(b) "
+		+ "WHERE a.id = $id "
+		+ "RETURN count(distinct b)";
 
-	return neo4jClient.queryPaginated(query, "b", countQuery, parameters("type", type, "id", id), pageable);
+		return neo4jClient.queryPaginated(query, "b", countQuery, parameters("type", type, "id", id), pageable);
     }
 
     public Page<JsonElement> recursivelyTraverseOutgoingEdges(String type, String id, List<String> edgeIRIs, Map<String,String> edgeProps, Pageable pageable) {
@@ -128,21 +133,21 @@ public Page<JsonElement> recursivelyTraverseOutgoingEdges(String type, String id
 
     public Page<JsonElement> recursivelyTraverseIncomingEdges(String type, String id, List<String> edgeIRIs, Map<String,String> edgeProps, Pageable pageable) {
 
-	String edge = makeEdgesList(edgeIRIs, Map.of());
+		String edge = makeEdgesList(edgeIRIs, Map.of());
 
-	String query =
-	  "MATCH (a:" + type + ") WHERE a.id = $id "
-	+ "WITH a "
-	+ "OPTIONAL MATCH (a)<-[edge:" + edge + " *]-(descendant) "
-	+ "RETURN DISTINCT descendant AS c";
+		String query =
+		  "MATCH (a:" + type + ") WHERE a.id = $id "
+		+ "WITH a "
+		+ "OPTIONAL MATCH (a)<-[edge:" + edge + " *]-(descendant) "
+		+ "RETURN DISTINCT descendant AS c";
 
-	String countQuery =
-	  "MATCH (a:" + type + ") WHERE a.id = $id "
-	+ "WITH a "
-	+ "OPTIONAL MATCH (a)<-[edge:" + edge + " *]-(descendant) "
-	+ "RETURN count(DISTINCT descendant)";
+		String countQuery =
+		  "MATCH (a:" + type + ") WHERE a.id = $id "
+		+ "WITH a "
+		+ "OPTIONAL MATCH (a)<-[edge:" + edge + " *]-(descendant) "
+		+ "RETURN count(DISTINCT descendant)";
 
-	return neo4jClient.queryPaginated(query, "c", countQuery, parameters("id", id), pageable);
+		return neo4jClient.queryPaginated(query, "c", countQuery, parameters("id", id), pageable);
     }
 
 

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/service/Neo4jClient.java b/backend/src/main/java/uk/ac/ebi/spot/ols/service/Neo4jClient.java
@@ -12,29 +12,31 @@
 import org.neo4j.driver.*;
 import org.neo4j.driver.Record;
 import org.neo4j.driver.exceptions.NoSuchRecordException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.stereotype.Component;
 import org.springframework.data.rest.webmvc.ResourceNotFoundException;
+import uk.ac.ebi.spot.ols.repository.neo4j.OlsNeo4jClient;
 
 import javax.validation.constraints.NotNull;
 
 @Component
 public class Neo4jClient {
 
-
 	@NotNull
 	@org.springframework.beans.factory.annotation.Value("${ols.neo4j.host:bolt://localhost:7687}")
 	private String host;
 
-
-
 	private Gson gson = new Gson();
 
 	private Driver driver;
 
+	private static final Logger logger = LoggerFactory.getLogger(Neo4jClient.class);
+
 	public Driver getDriver() {
 
 		if(driver == null) {
@@ -106,20 +108,20 @@ public Page<JsonElement> queryPaginated(String query, String resVar, String coun
 			queryToRun = query;
 		}
 
-		System.out.println(queryToRun);
-		System.out.println(gson.toJson(parameters.asMap()));
+		logger.debug(queryToRun);
+		logger.trace(gson.toJson(parameters.asMap()));
 
 		Stopwatch timer = Stopwatch.createStarted();
 		Result result = session.run(
 				queryToRun,
 
 		    parameters
 		);
-		System.out.println("Neo4j run paginated query: " + timer.stop());
+		logger.info("Neo4j run paginated query: " + timer.stop());
 
 		Stopwatch timer2 = Stopwatch.createStarted();
 		Result countResult = session.run(countQuery, parameters);
-		System.out.println("Neo4j run paginated count: " + timer2.stop());
+		logger.info("Neo4j run paginated count: " + timer2.stop());
 
 		Record countRecord = countResult.single();
 		int count = countRecord.get(0).asInt();
@@ -142,11 +144,11 @@ public JsonElement queryOne(String query, String resVar, Value parameters) {
 
 		Session session = getSession();
 
-		System.out.println(query);
+		logger.debug(query);
 
 		Stopwatch timer = Stopwatch.createStarted();
 		Result result = session.run(query, parameters);
-		System.out.println("Neo4j run query " + query + ": " + timer.stop());
+		logger.info("Neo4j run query " + query + ": " + timer.stop());
 
 		Value v = null;
 

diff --git a/backend/src/main/resources/logback.xml b/backend/src/main/resources/logback.xml
@@ -7,7 +7,7 @@
         </encoder>
     </appender>
 
-    <logger name="uk.ac.ebi.spot.ols" level="trace"/>
+    <logger name="uk.ac.ebi.spot.ols" level="info"/>
     <root level="error">
         <appender-ref ref="STDOUT" />
     </root>