1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/2ad3ef1aecc6/ changeset: 2ad3ef1aecc6 user: natefoo date: 2011-06-08 21:35:36 summary: Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. This changeset also makes it possible to upload compressed files that remain compressed (by choosing to "link files only"), however, Galaxy does not yet open the compressed file to properly set metadata on its contents. affected #: 1 file (1.1 KB)

--- a/tools/data_source/upload.py Wed Jun 08 15:30:40 2011 -0400 +++ b/tools/data_source/upload.py Wed Jun 08 15:35:36 2011 -0400 @@ -129,25 +129,29 @@ file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_gzipped and is_valid: - # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - gzipped_file = gzip.GzipFile( dataset.path, 'rb' ) - while 1: - try: - chunk = gzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing gzipped data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - gzipped_file.close() - # Replace the gzipped file with the decompressed file - shutil.move( uncompressed, dataset.path ) + 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 + 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: + try: + chunk = gzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing gzipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + gzipped_file.close() + # Replace the gzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) dataset.name = dataset.name.rstrip( '.gz' ) data_type = 'gzip' if not data_type and bz2 is not None: @@ -157,78 +161,86 @@ file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_bzipped and is_valid: - # We need to uncompress the temp_name file - CHUNK_SIZE = 2**20 # 1Mb - fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - bzipped_file = bz2.BZ2File( dataset.path, 'rb' ) - while 1: - try: - chunk = bzipped_file.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) - return - if not chunk: - break - os.write( fd, chunk ) - os.close( fd ) - bzipped_file.close() - # Replace the gzipped file with the decompressed file - shutil.move( uncompressed, dataset.path ) + if link_data_only == 'copy_files': + # We need to uncompress the temp_name file + 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: + try: + chunk = bzipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing bz2 compressed data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + bzipped_file.close() + # Replace the bzipped file with the decompressed file if it's safe to do so + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) dataset.name = dataset.name.rstrip( '.bz2' ) data_type = 'bz2' if not data_type: # See if we have a zip archive is_zipped = check_zip( dataset.path ) if is_zipped: - CHUNK_SIZE = 2**20 # 1Mb - uncompressed = None - uncompressed_name = None - unzipped = False - z = zipfile.ZipFile( dataset.path ) - for name in z.namelist(): - if name.endswith('/'): - continue - if unzipped: - 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 ) - if sys.version_info[:2] >= ( 2, 6 ): - zipped_file = z.open( name ) - while 1: + if link_data_only == 'copy_files': + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None + unzipped = False + z = zipfile.ZipFile( dataset.path ) + for name in z.namelist(): + if name.endswith('/'): + continue + if unzipped: + 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( output_path ), text=False ) + 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 - else: - # python < 2.5 doesn't have a way to read members in chunks(!) - try: - 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 - z.close() - # Replace the zipped file with the decompressed file - if uncompressed is not None: - shutil.move( uncompressed, dataset.path ) - dataset.name = uncompressed_name + z.close() + # Replace the zipped file with the decompressed file if it's safe to do so + if uncompressed is not None: + if dataset.type in ( 'server_dir', 'path_paste' ): + dataset.path = uncompressed + else: + shutil.move( uncompressed, dataset.path ) + dataset.name = uncompressed_name data_type = 'zip' if not data_type: if check_binary( dataset.path ): @@ -253,7 +265,7 @@ if data_type != 'binary': if link_data_only == 'copy_files': in_place = True - if dataset.type in ( 'server_dir', 'path_paste' ): + if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: in_place = False if dataset.space_to_tab: line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) @@ -277,7 +289,7 @@ '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' file_err( err_msg, dataset, json_file ) return - if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ): + if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: # Move the dataset to its "real" path if converted_path is not None: shutil.copy( converted_path, output_path ) @@ -362,7 +374,7 @@ add_file( dataset, registry, json_file, output_path ) # clean up paramfile try: - os.remove( sys.argv[1] ) + os.remove( sys.argv[3] ) except: pass

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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