🐛 Fix resource leaks causing CLOSE_WAIT connections

pom.xml

@@ -78,6 +78,10 @@
                     <groupId>junit</groupId>
                     <artifactId>junit</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>org.apache.commons</groupId>
+                    <artifactId>com.springsource.org.apache.commons.io</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
 
@@ -199,6 +203,11 @@
         </dependency>
 
         <!--Util-->
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.15.1</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>

src/main/java/org/reactome/server/service/controller/citation/CitationController.java

@@ -170,12 +170,11 @@ public void exportCitation(@PathVariable String id,
             response.setContentType(contentType);
             response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "\"");
 
-            InputStream in = new ByteArrayInputStream(citationString.getBytes(StandardCharsets.UTF_8));
-            OutputStream out = response.getOutputStream();
-            IOUtils.copy(in, out);
-            out.flush();
-            out.close();
-            in.close();
+            try (InputStream in = new ByteArrayInputStream(citationString.getBytes(StandardCharsets.UTF_8))) {
+                OutputStream out = response.getOutputStream();
+                IOUtils.copy(in, out);
+                out.flush();
+            }
         }
     }
 

src/main/java/org/reactome/server/service/controller/exporter/PptxExporterController.java

@@ -102,12 +102,11 @@ public synchronized void diagramPPTX(@Parameter(description = "Stable Identifier
         // when returning a FileSystemResource using Spring, then the file won't be deleted because it still has the
         // reference to the file and then we cannot delete. Writing the file directly in the response allows us to
         // delete only the temporary file.
-        OutputStream out = response.getOutputStream();
-        FileInputStream in = new FileInputStream(pptx);
-        IOUtils.copy(in, out);
-        out.flush();
-        out.close();
-        in.close();
+        try (FileInputStream in = new FileInputStream(pptx)) {
+            OutputStream out = response.getOutputStream();
+            IOUtils.copy(in, out);
+            out.flush();
+        }
 
         // deleting the file in case it is decorated.
         if (decorator.isDecorated() && !pptx.delete()) {
@@ -160,12 +159,11 @@ public synchronized void reactionPPTX(@Parameter(description = "DbId or StId of
         // when returning a FileSystemResource using Spring, then the file won't be deleted because it still has the
         // reference to the file and then we cannot delete. Writing the file directly in the response allows us to
         // delete only the temporary file.
-        OutputStream out = response.getOutputStream();
-        FileInputStream in = new FileInputStream(pptx);
-        IOUtils.copy(in, out);
-        out.flush();
-        out.close();
-        in.close();
+        try (FileInputStream in = new FileInputStream(pptx)) {
+            OutputStream out = response.getOutputStream();
+            IOUtils.copy(in, out);
+            out.flush();
+        }
 
         // deleting the file in case it is decorated.
         if (decorator.isDecorated() && !pptx.delete()) {

src/main/java/org/reactome/server/service/controller/exporter/SbxxExporterController.java

@@ -65,10 +65,11 @@ public synchronized void eventSBGN(@Parameter(description = "DbId or StId of the
         String fileName = event.getStId() + SBGN_FILE_EXTENSION;
         response.setContentType("application/sbgn+xml");
         response.setHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
-        OutputStream out = response.getOutputStream();
-        IOUtils.copy(getSBGN(event, fileName), out);
-        out.flush();
-        out.close();
+        try (InputStream sbgn = getSBGN(event, fileName)) {
+            OutputStream out = response.getOutputStream();
+            IOUtils.copy(sbgn, out);
+            out.flush();
+        }
     }
 
     private InputStream getSBGN(Event event, String fileName) throws FileNotFoundException {
@@ -106,10 +107,11 @@ public synchronized void eventSBML(@Parameter(description = "DbId or StId of the
         String fileName = event.getStId() + SBML_FILE_EXTENSION;
         response.setContentType("application/sbml+xml");
         response.setHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
-        OutputStream out = response.getOutputStream();
-        IOUtils.copy(getSBML(event, fileName), out);
-        out.flush();
-        out.close();
+        try (InputStream sbml = getSBML(event, fileName)) {
+            OutputStream out = response.getOutputStream();
+            IOUtils.copy(sbml, out);
+            out.flush();
+        }
     }
 
     private InputStream getSBML(Event event, String fileName) throws FileNotFoundException {