Use with statement in VcfGz class

galaxyproject · Aug 7, 2017 · 13d32ee · 13d32ee
1 parent 5cc71d2
commit 13d32ee
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
@@ -63,15 +63,15 @@ def displayable( self, dataset ):
             return False
 
     def get_chunk(self, trans, dataset, offset=0, ck_size=None):
-        f = compression_utils.get_fileobj(dataset.file_name)
-        f.seek(offset)
-        ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
-        if ck_data and ck_data[-1] != '\n':
-            cursor = f.read(1)
-            while cursor and cursor != '\n':
-                ck_data += cursor
+        with compression_utils.get_fileobj(dataset.file_name):
+            f.seek(offset)
+            ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
+            if ck_data and ck_data[-1] != '\n':
                 cursor = f.read(1)
-        last_read = f.tell()
+                while cursor and cursor != '\n':
+                    ck_data += cursor
+                    cursor = f.read(1)
+            last_read = f.tell()
         return dumps( { 'ck_data': util.unicodify( ck_data ),
                         'offset': last_read } )
 
@@ -1144,7 +1144,7 @@ def sniff(self, filename):
 
     def get_chunk(self, trans, dataset, chunk):
         ck_index = int(chunk)
-        f = compression_utils.get_fileobj(dataset.file_name)
+        f = open(dataset.file_name)
         f.seek(ck_index * trans.app.config.display_chunk_size)
         # If we aren't at the start of the file, seek to next newline.  Do this better eventually.
         if f.tell() != 0: