ALS-7883: Fix issues from checkmarx report

hms-dbmi · Nov 22, 2024 · cbc658b · cbc658b
1 parent 2772073
commit cbc658b
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Showing 12 changed files with 34 additions and 261 deletions.
diff --git a/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java b/pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Query.java
@@ -8,9 +8,13 @@
 import javax.persistence.*;
 
 import edu.harvard.dbmi.avillach.util.PicSureStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 @Entity(name = "query")
 public class Query extends BaseEntity {
+
+	private static final Logger logger = LoggerFactory.getLogger(Query.class);
 
 	//TODO may not need these two things
 	private Date startTime;
@@ -89,7 +93,7 @@ public String getQuery() {
 	          outStr += line;
 	        }
 		} catch (IOException e) {
-			e.printStackTrace();
+			throw new UncheckedIOException(e);
 		}
         return outStr;
 	}
@@ -106,7 +110,7 @@ public void setQuery(String queryStr) {
 	        gzip.close();
 	        this.query = obj.toByteArray();
 		} catch (IOException e) {
-			e.printStackTrace();
+			throw new UncheckedIOException(e);
 		}
 	}
 

diff --git a/...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java b/...sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/BaseRepository.java
@@ -142,13 +142,8 @@ public List<T> getByColumns(CriteriaQuery query, Root root, Predicate... predica
 		query.select(root);
 		if (predicates != null && predicates.length > 0)
 			query.where(predicates);
-		try{
-			return em().createQuery(query)
-					.getResultList();
-		} catch (PersistenceException e) {
-			e.printStackTrace();
-			return null;
-		}
+		return em().createQuery(query)
+				.getResultList();
 
 	}
 
@@ -168,9 +163,6 @@ public T getUniqueResultByColumns(CriteriaQuery query, Root root, Predicate... p
 				.getSingleResult();
 		} catch (NoResultException e){
 			return null;
-		} catch (PersistenceException e){
-			e.printStackTrace();
-			return null;
 		}
 	}
 

diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java
@@ -102,7 +102,7 @@ public String status() {
                     lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED;
                 }
             } catch (Exception e) {
-                e.printStackTrace();
+                logger.error("One or more components degraded", e);
                 lastStatus = ONE_OR_MORE_COMPONENTS_DEGRADED;
             }
             return lastStatus;

diff --git a/pic-sure-initializer/README.md b/pic-sure-initializer/README.md
diff --git a/pic-sure-initializer/pom.xml b/pic-sure-initializer/pom.xml
diff --git a/pic-sure-initializer/src/main/java/edu/harvard/hms/dbmi/avillach/PicSureInitializer.java b/pic-sure-initializer/src/main/java/edu/harvard/hms/dbmi/avillach/PicSureInitializer.java
diff --git a/pic-sure-initializer/src/main/resources/log4j.properties b/pic-sure-initializer/src/main/resources/log4j.properties
diff --git a/...ources/pic-sure-ga4gh-dos/src/main/java/edu/harvard/hms/dbmi/avillach/HttpClientUtil.java b/...ources/pic-sure-ga4gh-dos/src/main/java/edu/harvard/hms/dbmi/avillach/HttpClientUtil.java
@@ -1,31 +1,26 @@
 package edu.harvard.hms.dbmi.avillach;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.JsonNode;
-import org.apache.commons.io.IOUtils;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import edu.harvard.dbmi.avillach.util.exception.ResourceCommunicationException;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
-import org.apache.http.client.methods.HttpPost;
-import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.HttpClientBuilder;
-
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import edu.harvard.dbmi.avillach.util.exception.ResourceCommunicationException;
 import org.apache.http.util.EntityUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
 public class HttpClientUtil {
 	private final static ObjectMapper json = new ObjectMapper();
 
+	private static final Logger logger = LoggerFactory.getLogger(HttpClientUtil.class);
+
 	public static HttpResponse retrieveGetResponse(String uri, String token) {
 		try {
 			HttpClient client = HttpClientBuilder.create().build();
@@ -39,32 +34,6 @@ public static HttpResponse retrieveGetResponse(String uri, String token) {
 		}
 	}
 
-	public static HttpResponse retrievePostResponse(String uri, String token) {
-		try {
-			HttpClient client = HttpClientBuilder.create().build();
-			HttpPost post = new HttpPost(uri);
-            if (token != null) {
-                Map<String, String> clientCredentials = new HashMap<String, String>();
-                clientCredentials.put("BEARER_TOKEN", token);
-                post.setEntity(new StringEntity(json.writeValueAsString(clientCredentials)));
-            }
-			post.setHeader("Content-type","application/json");
-			return client.execute(post);
-		} catch (IOException e) {
-			throw new ResourceCommunicationException(uri, e);
-		}
-	}
-
-	public static <T> List<T> readListFromResponse(HttpResponse response, Class<T> expectedElementType) {
-		try {
-			String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
-			return json.readValue(responseBody, new TypeReference<List<T>>() {});
-		} catch (IOException e) {
-			e.printStackTrace();
-			return new ArrayList<T>();
-		}
-	}
-
 	public static <T> List<T> readDataObjectsFromResponse(HttpResponse response, Class<T> expectedElementType) {
 		try {
 			String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
@@ -79,7 +48,7 @@ public static <T> List<T> readDataObjectsFromResponse(HttpResponse response, Cla
                 return json.readValue(jn.get("data_objects").toString(), new TypeReference<List<T>>() {});
             }
 		} catch (IOException e) {
-			e.printStackTrace();
+			logger.error("Error reading object from response, returning empty list", e);
 			return new ArrayList<T>();
 		}
 	}

diff --git a/...a/edu/harvard/hms/dbmi/avillach/resource/visualization/service/DataProcessingService.java b/...a/edu/harvard/hms/dbmi/avillach/resource/visualization/service/DataProcessingService.java
@@ -283,7 +283,6 @@ private String createXAxisLabel(String title) {
             return title.substring(title.lastIndexOf(" ") + 1);
         } catch (IndexOutOfBoundsException e) {
             logger.error("Error getting cross counts: " + e.getMessage());
-            e.printStackTrace();
             return title;
         }
     }

diff --git a/.../java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java b/.../java/edu/harvard/dbmi/avillach/util/exception/mapper/IllegalArgumentExceptionMapper.java
@@ -1,6 +1,8 @@
 package edu.harvard.dbmi.avillach.util.exception.mapper;
 
 import edu.harvard.dbmi.avillach.util.response.PICSUREResponse;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.ws.rs.core.Response;
 import javax.ws.rs.ext.ExceptionMapper;
@@ -9,9 +11,11 @@
 @Provider
 public class IllegalArgumentExceptionMapper implements ExceptionMapper<IllegalArgumentException>{
 
+    private static final Logger logger = LoggerFactory.getLogger(IllegalArgumentExceptionMapper.class);
+
     @Override
     public Response toResponse(IllegalArgumentException exception) {
-        exception.printStackTrace();
+        logger.error("Uncaught exception", exception);
         return PICSUREResponse.protocolError(exception.getMessage());
     }
 }