def stage_file(name, composite_file_path, is_binary=False):
dp = composite_file_path['path']
path, is_url = to_path(dp)
if is_url:
dataset.path = path
dp = path
auto_decompress = composite_file_path.get('auto_decompress', True)
if auto_decompress and not datatype.composite_type and CompressedFile.can_decompress(
dp):
# It isn't an explictly composite datatype, so these are just extra files to attach
# as composite data. It'd be better if Galaxy was communicating this to the tool
# a little more explicitly so we didn't need to dispatch on the datatype and so we
# could attach arbitrary extra composite data to an existing composite datatype if
# if need be? Perhaps that would be a mistake though.
CompressedFile(dp).extract(files_path)
else:
if not is_binary:
tmpdir = output_adjacent_tmpdir(output_path)
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
if composite_file_path.get('space_to_tab'):
sniff.convert_newlines_sep2tabs(dp,
tmp_dir=tmpdir,
tmp_prefix=tmp_prefix)
else:
sniff.convert_newlines(dp,
tmp_dir=tmpdir,
tmp_prefix=tmp_prefix)
file_output_path = os.path.join(files_path, name)
shutil.move(dp, file_output_path)
# groom the dataset file content if required by the corresponding datatype definition
if datatype.dataset_content_needs_grooming(file_output_path):
datatype.groom_dataset_content(file_output_path)
def stage_file(name, composite_file_path, is_binary=False):
dp = composite_file_path['path']
path, is_url = to_path(dp)
if is_url:
dataset.path = path
dp = path
auto_decompress = composite_file_path.get('auto_decompress', True)
if auto_decompress and not datatype.composite_type and CompressedFile.can_decompress(
dp):
# It isn't an explicitly composite datatype, so these are just extra files to attach
# as composite data. It'd be better if Galaxy was communicating this to the tool
# a little more explicitly so we didn't need to dispatch on the datatype and so we
# could attach arbitrary extra composite data to an existing composite datatype if
# if need be? Perhaps that would be a mistake though.
CompressedFile(dp).extract(files_path)
else:
tmpdir = output_adjacent_tmpdir(output_path)
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
sniff.handle_composite_file(
datatype,
dp,
files_path,
name,
is_binary,
tmpdir,
tmp_prefix,
composite_file_path,
)
def stage_file(name, composite_file_path, is_binary=False):
dp = composite_file_path['path']
path, is_url = to_path(dp)
if is_url:
dataset.path = path
dp = path
auto_decompress = composite_file_path.get('auto_decompress', True)
if auto_decompress and not datatype.composite_type and CompressedFile.can_decompress(dp):
# It isn't an explictly composite datatype, so these are just extra files to attach
# as composite data. It'd be better if Galaxy was communicating this to the tool
# a little more explicitly so we didn't need to dispatch on the datatype and so we
# could attach arbitrary extra composite data to an existing composite datatype if
# if need be? Perhaps that would be a mistake though.
CompressedFile(dp).extract(files_path)
else:
if not is_binary:
tmpdir = output_adjacent_tmpdir(output_path)
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
if composite_file_path.get('space_to_tab'):
sniff.convert_newlines_sep2tabs(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
else:
sniff.convert_newlines(dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix)
file_output_path = os.path.join(files_path, name)
shutil.move(dp, file_output_path)
# groom the dataset file content if required by the corresponding datatype definition
if datatype.dataset_content_needs_grooming(file_output_path):
datatype.groom_dataset_content(file_output_path)