opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

"Fix" zip uploads for Python < 2.6. The scare quotes are because in Python < 2.6 you can't read a zip member without loading the entire member into memory...

Browse Source
This commit is contained in:
Nate Coraor
2010-10-25 16:10:09 -04:00
parent a9520cc626
commit 8367cdc4a6
1 changed files with 24 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/data_source/upload.py
+24 -10
View File
@@ -270,22 +270,36 @@ def add_file( dataset, registry, json_file, output_path ):
stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.'
break
fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False )
zipped_file = z.open( name )
while 1:
if sys.version_info[:2] >= ( 2, 6 ):
zipped_file = z.open( name )
while 1:
try:
chunk = zipped_file.read( CHUNK_SIZE )
except IOError:
os.close( fd )
os.remove( uncompressed )
file_err( 'Problem decompressing zipped data', dataset, json_file )
return
if not chunk:
break
os.write( fd, chunk )
os.close( fd )
zipped_file.close()
uncompressed_name = name
unzipped = True
else:
# python < 2.5 doesn't have a way to read members in chunks(!)
try:
chunk = zipped_file.read( CHUNK_SIZE )
outfile = open( uncompressed, 'wb' )
outfile.write( z.read( name ) )
outfile.close()
uncompressed_name = name
unzipped = True
except IOError:
os.close( fd )
os.remove( uncompressed )
file_err( 'Problem decompressing zipped data', dataset, json_file )
return
if not chunk:
break
os.write( fd, chunk )
os.close( fd )
zipped_file.close()
uncompressed_name = name
unzipped = True
z.close()
# Replace the zipped file with the decompressed file
if uncompressed is not None: