diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index b3de1f5a97a..4afad30d276 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -393,8 +393,10 @@ class Ms2(Text):
         header_lines = []
         while True:
             line = contents.readline()
-            if line is None or len(line) == 0:
-                pass
+            if not line:
+                return False
+            if line.strip() == "":
+                continue
             elif line.startswith('H\t'):
                 header_lines.append(line)
             else:
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index e89b24c3380..b0fb78fe812 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -290,6 +290,9 @@ def guess_ext(fname, sniff_order, is_binary=False):
     >>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
     >>> datatypes_registry = example_datatype_registry_for_sample()
     >>> sniff_order = datatypes_registry.sniff_order
+    >>> fname = get_test_fname('empty.txt')
+    >>> guess_ext(fname, sniff_order)
+    'txt'
     >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
     >>> guess_ext(fname, sniff_order)
     'blastxml'
diff --git a/lib/galaxy/datatypes/test/empty.txt b/lib/galaxy/datatypes/test/empty.txt
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 6b4f636d7da..3e05aef66e9 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -108,7 +108,7 @@ def add_file(dataset, registry, output_path):
     if not os.path.exists(dataset.path):
         raise UploadProblemException('Uploaded temporary file (%s) does not exist.' % dataset.path)
 
-    if not os.path.getsize(dataset.path) > 0:
+    if check_content and not os.path.getsize(dataset.path) > 0:
         raise UploadProblemException('The uploaded file is empty')
 
     stdout, ext, datatype, is_binary, converted_path = handle_upload(