Fix biojava#933 URLConnection to invalid HTTP URL is not detected as failure

aalhossary · aalhossary · commit 0a66b4ec102e · 2021-06-17T02:11:09.000+08:00
When the httpConnection is invalid, the application does not detect it, and it saves an empty (precisely a 20 bytes) file. This fix detects when the connection is invalid or the file has no contents. Related to biojava#703
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -14,7 +14,6 @@
 import java.io.FileOutputStream;
 import java.io.FilenameFilter;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.io.StringWriter;
@@ -320,8 +319,13 @@ private static boolean downloadChemCompRecord(String recordName) {
             try (PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(newFile)));
                  BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()))) {
                 String line;
+                boolean success = false;
                 while ((line = fileBuffer.readLine()) != null) {
                     pw.println(line);
+                    success = true;
+                }
+                if(!success) {
+                	throw new IOException("Could not read from URL "+url.toString());
                 }
 
                 pw.flush();
