closing unhandled tar

Author: vsoch

singularity/analysis/compare.py

@@ -128,13 +128,13 @@ def compare_singularity_images(image_paths1,image_paths2=None):
                     members2 = [x.name for x in tar2]
                     c = compare_lists(members1,members2)
                     sim = information_coefficient(c['total1'],c['total2'],c['intersect'])
-                    delete_image_tar(fileobj2)
+                    delete_image_tar(fileobj2, tar2)
 
                 dfs.loc[image1,image2] = sim
                 if repeat:
                     dfs.loc[image2,image1] = sim
                 comparisons_done.append(comparison_id)
-        delete_image_tar(fileobj1)
+        delete_image_tar(fileobj1, tar1)
     return dfs
 
 

singularity/analysis/reproduce/hash.py

@@ -99,7 +99,7 @@ def get_image_hash(image_path,
                                 include_files=include_files)
 
     cli = Singularity()
-    file_obj,tar = get_image_tar(image_path)
+    file_obj, tar = get_image_tar(image_path)
     hasher = hashlib.md5()
 
     for member in tar:
@@ -117,11 +117,14 @@ def get_image_hash(image_path,
 
     digest = hasher.hexdigest()
 
-    if isinstance(file_obj,io.BytesIO):
+    # Close up / remove files
+    try:
         file_obj.close()
-    else:
-        if os.path.exists(file_obj):
-            os.remove(file_obj)
+    except:
+        tar.close()
+ 
+    if os.path.exists(file_obj):
+        os.remove(file_obj)
 
     return digest
 
@@ -163,7 +166,7 @@ def get_content_hashes(image_path,
                            tag_root=tag_root,
                            include_sizes=include_sizes)
 
-    deleted = delete_image_tar(file_obj)
+    delete_image_tar(file_obj, tar)
     return results
 
 

singularity/analysis/reproduce/utils.py

@@ -114,19 +114,17 @@ def get_image_tar(image_path,S=None):
     return file_obj, tar
 
 
-def delete_image_tar(file_obj):
+def delete_image_tar(file_obj, tar):
     '''delete image tar will close a file object (if extracted into
     memory) or delete from the file system (if saved to disk)'''
-    deleted = False
-    if isinstance(file_obj,io.BytesIO):
+    try:
         file_obj.close()
+    except:
+        tar.close()
+    if os.path.exists(file_obj):
+        os.remove(file_obj)
         deleted = True
-        bot.debug('Closed memory tar.')   
-    else:
-        if os.path.exists(file_obj):
-            os.remove(file_obj)
-            deleted = True
-            bot.debug('Deleted temporary tar.')   
+        bot.debug('Deleted temporary tar.')   
     return deleted
 
 

singularity/cli/__init__.py

@@ -61,7 +61,10 @@ def run_command(self, cmd, sudo=False, quiet=False):
                 try:
                     message=message.decode('utf-8')
                 except UnicodeDecodeError:
-                    message = unicode(message, errors='replace')
+                    try:
+                        message = unicode(message, errors='replace')
+                    except NameError:
+                        message = str(message, errors='replace')
             return message
         if quiet is False:
             bot.error("Return Code %s: %s" %(return_code,

singularity/package/build.py

@@ -164,7 +164,7 @@ def package(image_path,
     zipfile = zip_up(to_package,zip_name=zip_name,output_folder=output_folder)
     bot.debug("Package created at %s" %(zipfile))
 
-    if not delete_image_tar(file_obj):
+    if not delete_image_tar(file_obj, tar):
         bot.warning("Could not clean up temporary tarfile.")
 
     # return package to user

singularity/tests/test_reproduce.py

@@ -146,6 +146,7 @@ def test_extract_guts(self):
                             file_filter=levels['REPLICATE'])
         for key in ['root_owned','sizes','hashes']:
             self.assertTrue(key in guts)
+        tar.close()
 
     def test_get_image_file_hash(self):
         from singularity.analysis.reproduce import get_image_file_hash