Merge pull request #99 from nitin-ebi/internalservererror

EVA-2911 - Handle exception when trying to disconnect
EBIvariation · Jun 30, 2022 · eeaa806 · eeaa806
2 parents 3a5c3c8 + e0a1512
commit eeaa806
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Showing 3 changed files with 19 additions and 4 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/datasource/ENAAssemblyDataSource.java b/src/main/java/uk/ac/ebi/eva/contigalias/datasource/ENAAssemblyDataSource.java
@@ -28,7 +28,6 @@
 import uk.ac.ebi.eva.contigalias.entities.ChromosomeEntity;
 import uk.ac.ebi.eva.contigalias.entities.ScaffoldEntity;
 import uk.ac.ebi.eva.contigalias.entities.SequenceEntity;
-import uk.ac.ebi.eva.contigalias.service.AssemblyService;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -70,7 +69,11 @@ public Optional<AssemblyEntity> getAssemblyByAccession(String accession) throws
             ENAAssemblyReportReader reader = readerFactory.build(stream);
             assemblyEntity = reader.getAssemblyEntity();
         } finally {
-            enaBrowser.disconnect();
+            try {
+                enaBrowser.disconnect();
+            } catch (IOException e){
+                logger.warn("Error while trying to disconnect - enaBrowser (assembly: " + accession + ") : " + e);
+            }
         }
         return Optional.of(assemblyEntity);
     }

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java b/src/main/java/uk/ac/ebi/eva/contigalias/datasource/NCBIAssemblyDataSource.java
@@ -16,6 +16,8 @@
 
 package uk.ac.ebi.eva.contigalias.datasource;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
@@ -32,6 +34,8 @@
 @Repository("NCBIDataSource")
 public class NCBIAssemblyDataSource implements AssemblyDataSource {
 
+    private final Logger logger = LoggerFactory.getLogger(NCBIAssemblyDataSource.class);
+
     private final NCBIBrowserFactory factory;
 
     private final NCBIAssemblyReportReaderFactory readerFactory;
@@ -57,7 +61,11 @@ public Optional<AssemblyEntity> getAssemblyByAccession(
             NCBIAssemblyReportReader reader = readerFactory.build(stream);
             assemblyEntity = reader.getAssemblyEntity();
         } finally {
-            ncbiBrowser.disconnect();
+            try {
+                ncbiBrowser.disconnect();
+            } catch (IOException e) {
+                logger.warn("Error while trying to disconnect - ncbiBrowser (assembly: " + accession + ") : " + e);
+            }
         }
         return Optional.of(assemblyEntity);
     }

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/dus/PassiveAnonymousFTPClient.java b/src/main/java/uk/ac/ebi/eva/contigalias/dus/PassiveAnonymousFTPClient.java
@@ -60,7 +60,11 @@ public void connect(String address, int port) throws IOException {
             logger.info("Connected successfully to {}", address);
         } catch (Exception e) {
             logger.error("Could not connect to FTP server '{}'. {}.", address, getStatusString());
-            this.disconnect();
+            try {
+                this.disconnect();
+            } catch (IOException ex) {
+                logger.warn("Error while trying to disconnect : " + ex);
+            }
             throw e;
         }
     }