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This commit is contained in:
Trevor Wennblom
2014-02-20 18:14:09 -06:00
parent 85add8fc6d
commit 1848cf2e3d
7 changed files with 37 additions and 37 deletions
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tools/data_source/upload.py
+2 -2
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@@ -126,7 +126,7 @@ def add_file( dataset, registry, json_file, output_path ):
elif is_gzipped and is_valid:
if link_data_only == 'copy_files':
# We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
CHUNK_SIZE = 2**20 # 1Mb
CHUNK_SIZE = 2**20 # 1Mb
fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
gzipped_file = gzip.GzipFile( dataset.path, 'rb' )
while 1:
@@ -159,7 +159,7 @@ def add_file( dataset, registry, json_file, output_path ):
elif is_bzipped and is_valid:
if link_data_only == 'copy_files':
# We need to uncompress the temp_name file
CHUNK_SIZE = 2**20 # 1Mb
CHUNK_SIZE = 2**20 # 1Mb
fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
bzipped_file = bz2.BZ2File( dataset.path, 'rb' )
while 1: