From 6d4d6dd91ae82d9a327b8283342e5105c075076a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 10 Jun 2014 09:36:28 -0500
Subject: [PATCH] Bugfix: Fix shutil.move for converted files in upload.py.

---
 lib/galaxy/datatypes/sniff.py |  8 ++++----
 tools/data_source/upload.py   | 21 +++++++++++++++++----
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 7d64e386c1f..e35931c04b3 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -90,7 +90,7 @@ def check_newlines( fname, bytes_to_read=52428800 ):
     f.close()
     return False
 
-def convert_newlines( fname, in_place=True ):
+def convert_newlines( fname, in_place=True, tmp_dir=None, tmp_prefix=None ):
     """
     Converts in place a file from universal line endings
     to Posix line endings.
@@ -102,7 +102,7 @@ def convert_newlines( fname, in_place=True ):
     >>> file(fname).read()
     '1 2\\n3 4\\n'
     """
-    fd, temp_name = tempfile.mkstemp()
+    fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir )
     fp = os.fdopen( fd, "wt" )
     i = None
     for i, line in enumerate( file( fname, "U" ) ):
@@ -150,7 +150,7 @@ def sep2tabs( fname, in_place=True, patt="\\s+" ):
     else:
         return ( i, temp_name )
 
-def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ):
+def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix=None ):
     """
     Combines above methods: convert_newlines() and sep2tabs()
     so that files do not need to be read twice
@@ -163,7 +163,7 @@ def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ):
     '1\\t2\\n3\\t4\\n'
     """
     regexp = re.compile( patt )
-    fd, temp_name = tempfile.mkstemp()
+    fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir )
     fp = os.fdopen( fd, "wt" )
     for i, line in enumerate( file( fname, "U" ) ):
         line  = line.rstrip( '\r\n' )
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 4d5a0a1ff90..f3911191288 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -272,10 +272,12 @@ def add_file( dataset, registry, json_file, output_path ):
                 # so that is becomes possible to upload gzip, bz2 or zip files with binary data without
                 # corrupting the content of those files.
                 if dataset.to_posix_lines:
+                    tmpdir = output_adjacent_tmpdir( output_path )
+                    tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
                     if dataset.space_to_tab:
-                        line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place )
+                        line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
                     else:
-                        line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )
+                        line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
             if dataset.file_type == 'auto':
                 ext = sniff.guess_ext( dataset.path, registry.sniff_order )
             else:
@@ -343,10 +345,12 @@ def add_composite_file( dataset, registry, json_file, output_path, files_path ):
                        dataset.path = temp_name
                        dp = temp_name
                     if not value.is_binary:
+                        tmpdir = output_adjacent_tmpdir( output_path )
+                        tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
                         if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ):
-                            sniff.convert_newlines_sep2tabs( dp )
+                            sniff.convert_newlines_sep2tabs( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
                         else:
-                            sniff.convert_newlines( dp )
+                            sniff.convert_newlines( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
                     shutil.move( dp, os.path.join( files_path, name ) )
         # Move the dataset to its "real" path
         shutil.move( dataset.primary_file, output_path )
@@ -356,6 +360,15 @@ def add_composite_file( dataset, registry, json_file, output_path, files_path ):
                      stdout = 'uploaded %s file' % dataset.file_type )
         json_file.write( to_json_string( info ) + "\n" )
 
+
+def output_adjacent_tmpdir( output_path ):
+    """ For temp files that will ultimately be moved to output_path anyway
+    just create the file directly in output_path's directory so shutil.move
+    will work optimially.
+    """
+    return os.path.dirname( output_path )
+
+
 def __main__():
 
     if len( sys.argv ) < 4: