def process_move(self,
data_table_name,
column_name,
source_base_path,
relative_symlinks=False,
**kwd):
if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[
data_table_name]:
move_dict = self.move_by_data_table_column[data_table_name][
column_name]
source = move_dict['source_base']
if source is None:
source = source_base_path
else:
source = fill_template(
source,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.
config.galaxy_data_manager_data_path,
**kwd)
if move_dict['source_value']:
source = os.path.join(
source,
fill_template(
move_dict['source_value'],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.
config.galaxy_data_manager_data_path,
**kwd))
target = move_dict['target_base']
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template(
target,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.
config.galaxy_data_manager_data_path,
**kwd)
if move_dict['target_value']:
target = os.path.join(
target,
fill_template(
move_dict['target_value'],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.
config.galaxy_data_manager_data_path,
**kwd))
if move_dict['type'] == 'file':
dirs = os.path.split(target)[0]
try:
os.makedirs(dirs)
except OSError as e:
if e.errno != errno.EEXIST:
raise e
# moving a directory and the target already exists, we move the contents instead
util.move_merge(source, target)
if move_dict.get('relativize_symlinks', False):
util.relativize_symlinks(target)
return True
return False
def process_move(self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd):
if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[data_table_name]:
move_dict = self.move_by_data_table_column[data_table_name][column_name]
source = move_dict['source_base']
if source is None:
source = source_base_path
else:
source = fill_template(source, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
if move_dict['source_value']:
source = os.path.join(source, fill_template(move_dict['source_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
target = move_dict['target_base']
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template(target, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip()
if move_dict['target_value']:
target = os.path.join(target, fill_template(move_dict['target_value'], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd).strip())
if move_dict['type'] == 'file':
dirs = os.path.split(target)[0]
try:
os.makedirs(dirs)
except OSError as e:
if e.errno != errno.EEXIST:
raise e
# moving a directory and the target already exists, we move the contents instead
if os.path.exists(source):
util.move_merge(source, target)
if move_dict.get('relativize_symlinks', False):
util.relativize_symlinks(target)
return True
return False
def process_move(self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd):
if (
data_table_name in self.move_by_data_table_column
and column_name in self.move_by_data_table_column[data_table_name]
):
move_dict = self.move_by_data_table_column[data_table_name][column_name]
source = move_dict["source_base"]
if source is None:
source = source_base_path
else:
source = fill_template(
source,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
)
if move_dict["source_value"]:
source = os.path.join(
source,
fill_template(
move_dict["source_value"],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
),
)
target = move_dict["target_base"]
if target is None:
target = self.data_managers.app.config.galaxy_data_manager_data_path
else:
target = fill_template(
target,
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
)
if move_dict["target_value"]:
target = os.path.join(
target,
fill_template(
move_dict["target_value"],
GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path,
**kwd
),
)
if move_dict["type"] == "file":
dirs, filename = os.path.split(target)
try:
os.makedirs(dirs)
except OSError, e:
if e.errno != errno.EEXIST:
raise e
# log.debug( 'Error creating directory "%s": %s' % ( dirs, e ) )
# moving a directory and the target already exists, we move the contents instead
util.move_merge(source, target)
if move_dict.get("relativize_symlinks", False):
util.relativize_symlinks(target)
return True