Remove erroneous exceptions from Scop

sbliven · sbliven · commit b86d92a704dc · 2014-02-17T18:55:03.000+01:00
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/ScopInstallation.java
@@ -701,6 +701,7 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
+		IOException exception = null;
 		for(ScopURLs mirror:mirrors) {
 			try {
 				URL url = new URL(mirror.getClaURL(scopVersion));
@@ -709,18 +710,20 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{
 				File localFile = new File(localFileName);
 
 				downloadFileFromRemote(url, localFile);
-				break;
+				return;
 			} catch(IOException e ) {
+				exception = e;
 				continue;
 			}
 		}
-		throw new IOException("Unable to download SCOP .cla file");
+		throw new IOException("Unable to download SCOP .cla file",exception);
 	}
 
 	protected void downloadDesFile() throws FileNotFoundException, IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
+		IOException exception = null;
 		for(ScopURLs mirror:mirrors) {
 			try {
 				URL url = new URL(mirror.getDesURL( scopVersion));
@@ -729,18 +732,20 @@ protected void downloadDesFile() throws FileNotFoundException, IOException{
 				File localFile = new File(localFileName);
 
 				downloadFileFromRemote(url, localFile);
-				break;
+				return;
 			} catch(IOException e ) {
+				exception = e;
 				continue;
 			}
 		}
-		throw new IOException("Unable to download SCOP .des file");
+		throw new IOException("Unable to download SCOP .des file",exception);
 	}
 
 	protected void downloadHieFile() throws FileNotFoundException, IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
+		IOException exception = null;
 		for(ScopURLs mirror:mirrors) {
 			try {
 				URL url = new URL(mirror.getHieURL( scopVersion));
@@ -749,19 +754,21 @@ protected void downloadHieFile() throws FileNotFoundException, IOException{
 				File localFile = new File(localFileName);
 
 				downloadFileFromRemote(url, localFile);
-				break;
+				return;
 			} catch(IOException e ) {
+				exception = e;
 				continue;
 			}
 		}
-		throw new IOException("Unable to download SCOP .hie file");
+		throw new IOException("Unable to download SCOP .hie file",exception);
 
 	}
 
 	protected void downloadComFile() throws FileNotFoundException, IOException{
 		if(mirrors.size()<1) {
 			initScopURLs();
 		}
+		IOException exception = null;
 		for(ScopURLs mirror:mirrors) {
 			try {
 				URL url = new URL(mirror.getComURL(scopVersion));
@@ -770,14 +777,13 @@ protected void downloadComFile() throws FileNotFoundException, IOException{
 				File localFile = new File(localFileName);
 
 				downloadFileFromRemote(url, localFile);
-				break;
+				return;
 			} catch(IOException e ) {
+				exception = e;
 				continue;
 			}
 		}
-		throw new IOException("Unable to download SCOP .com file");
-
-
+		throw new IOException("Unable to download SCOP .com file",exception);
 	}
 
 	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{

Original file line number	Diff line number	Diff line change
`@@ -701,6 +701,7 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{`
`701`	`701`	`if(mirrors.size()<1) {`
`702`	`702`	`initScopURLs();`
`703`	`703`	`}`
	`704`	`+ IOException exception = null;`
`704`	`705`	`for(ScopURLs mirror:mirrors) {`
`705`	`706`	`try {`
`706`	`707`	`URL url = new URL(mirror.getClaURL(scopVersion));`
`@@ -709,18 +710,20 @@ protected void downloadClaFile() throws FileNotFoundException, IOException{`
`709`	`710`	`File localFile = new File(localFileName);`
`710`	`711`
`711`	`712`	`downloadFileFromRemote(url, localFile);`
`712`		`- break;`
	`713`	`+ return;`
`713`	`714`	`} catch(IOException e ) {`
	`715`	`+ exception = e;`
`714`	`716`	`continue;`
`715`	`717`	`}`
`716`	`718`	`}`
`717`		`- throw new IOException("Unable to download SCOP .cla file");`
	`719`	`+ throw new IOException("Unable to download SCOP .cla file",exception);`
`718`	`720`	`}`
`719`	`721`
`720`	`722`	`protected void downloadDesFile() throws FileNotFoundException, IOException{`
`721`	`723`	`if(mirrors.size()<1) {`
`722`	`724`	`initScopURLs();`
`723`	`725`	`}`
	`726`	`+ IOException exception = null;`
`724`	`727`	`for(ScopURLs mirror:mirrors) {`
`725`	`728`	`try {`
`726`	`729`	`URL url = new URL(mirror.getDesURL( scopVersion));`
`@@ -729,18 +732,20 @@ protected void downloadDesFile() throws FileNotFoundException, IOException{`
`729`	`732`	`File localFile = new File(localFileName);`
`730`	`733`
`731`	`734`	`downloadFileFromRemote(url, localFile);`
`732`		`- break;`
	`735`	`+ return;`
`733`	`736`	`} catch(IOException e ) {`
	`737`	`+ exception = e;`
`734`	`738`	`continue;`
`735`	`739`	`}`
`736`	`740`	`}`
`737`		`- throw new IOException("Unable to download SCOP .des file");`
	`741`	`+ throw new IOException("Unable to download SCOP .des file",exception);`
`738`	`742`	`}`
`739`	`743`
`740`	`744`	`protected void downloadHieFile() throws FileNotFoundException, IOException{`
`741`	`745`	`if(mirrors.size()<1) {`
`742`	`746`	`initScopURLs();`
`743`	`747`	`}`
	`748`	`+ IOException exception = null;`
`744`	`749`	`for(ScopURLs mirror:mirrors) {`
`745`	`750`	`try {`
`746`	`751`	`URL url = new URL(mirror.getHieURL( scopVersion));`
`@@ -749,19 +754,21 @@ protected void downloadHieFile() throws FileNotFoundException, IOException{`
`749`	`754`	`File localFile = new File(localFileName);`
`750`	`755`
`751`	`756`	`downloadFileFromRemote(url, localFile);`
`752`		`- break;`
	`757`	`+ return;`
`753`	`758`	`} catch(IOException e ) {`
	`759`	`+ exception = e;`
`754`	`760`	`continue;`
`755`	`761`	`}`
`756`	`762`	`}`
`757`		`- throw new IOException("Unable to download SCOP .hie file");`
	`763`	`+ throw new IOException("Unable to download SCOP .hie file",exception);`
`758`	`764`
`759`	`765`	`}`
`760`	`766`
`761`	`767`	`protected void downloadComFile() throws FileNotFoundException, IOException{`
`762`	`768`	`if(mirrors.size()<1) {`
`763`	`769`	`initScopURLs();`
`764`	`770`	`}`
	`771`	`+ IOException exception = null;`
`765`	`772`	`for(ScopURLs mirror:mirrors) {`
`766`	`773`	`try {`
`767`	`774`	`URL url = new URL(mirror.getComURL(scopVersion));`
`@@ -770,14 +777,13 @@ protected void downloadComFile() throws FileNotFoundException, IOException{`
`770`	`777`	`File localFile = new File(localFileName);`
`771`	`778`
`772`	`779`	`downloadFileFromRemote(url, localFile);`
`773`		`- break;`
	`780`	`+ return;`
`774`	`781`	`} catch(IOException e ) {`
	`782`	`+ exception = e;`
`775`	`783`	`continue;`
`776`	`784`	`}`
`777`	`785`	`}`
`778`		`- throw new IOException("Unable to download SCOP .com file");`
`779`		`-`
`780`		`-`
	`786`	`+ throw new IOException("Unable to download SCOP .com file",exception);`
`781`	`787`	`}`
`782`	`788`
`783`	`789`	`protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{`