From e632e27a0fba2bb789ba055f3e06f90cab0082e6 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 30 Aug 2013 11:49:37 +0100
Subject: [PATCH] check to ensure not recursively trying to read from the same
file
---
.../artemis/components/UserDefinedQualifiers.java | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
index 0030834ee..9d4544fb3 100644
--- a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
+++ b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
@@ -479,7 +479,7 @@ class UserDefinedQualifiers extends JFrame
*/
private QualifierVector loadQualifiers(final Document doc) throws IOException
{
- QualifierVector qualifiers = loadObo(doc.getInputStream());
+ QualifierVector qualifiers = loadObo(doc);
if(qualifiers.size() == 0)
qualifiers = loadText(doc.getInputStream());
return qualifiers;
@@ -489,11 +489,12 @@ class UserDefinedQualifiers extends JFrame
* Load in qualifiers from an input stream that are in OBO format.
* @param ins
* @return
+ * @throws IOException
*/
- private QualifierVector loadObo(final InputStream ins)
+ private QualifierVector loadObo(final Document doc) throws IOException
{
final LinePushBackReader reader = new LinePushBackReader(
- new BufferedReader(new InputStreamReader(ins)));
+ new BufferedReader(new InputStreamReader(doc.getInputStream())));
final QualifierVector qualifiers = new QualifierVector();
try
{
@@ -539,8 +540,11 @@ class UserDefinedQualifiers extends JFrame
else if(line.startsWith("import:"))
{
// import OBO file from a URL
- final URL url = new URL(line.substring(7).trim());
- createObo(new URLDocument(url));
+ final URLDocument urlDoc = new URLDocument(
+ new URL(line.substring(7).trim()) );
+ // check to ensure not recursively reading from same file
+ if(!doc.getLocation().equals(urlDoc.getLocation()))
+ createObo(urlDoc);
}
}
reader.close();
--
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