def _upload_dataset(self, trans, library_id, folder_id, replace_dataset=None, **kwd):
# Set up the traditional tool state/params
cntrller = 'api'
tool_id = 'upload1'
message = None
file_type = kwd.get('file_type')
try:
upload_common.validate_datatype_extension(datatypes_registry=trans.app.datatypes_registry, ext=file_type)
except RequestParameterInvalidException as e:
return (400, util.unicodify(e))
tool = trans.app.toolbox.get_tool(tool_id)
state = tool.new_state(trans)
populate_state(trans, tool.inputs, kwd, state.inputs)
tool_params = state.inputs
dataset_upload_inputs = []
for input_name, input in tool.inputs.items():
if input.type == "upload_dataset":
dataset_upload_inputs.append(input)
# Library-specific params
server_dir = kwd.get('server_dir', '')
upload_option = kwd.get('upload_option', 'upload_file')
response_code = 200
if upload_option == 'upload_directory':
full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
message = 'Select a directory'
elif upload_option == 'upload_paths':
# Library API already checked this - following check isn't actually needed.
validate_path_upload(trans)
# Some error handling should be added to this method.
try:
# FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd
# should be passed so that complex objects that may have been included in the initial request remain.
library_bunch = upload_common.handle_library_params(trans, kwd, folder_id, replace_dataset)
except Exception:
response_code = 500
message = "Unable to parse upload parameters, please report this error."
# Proceed with (mostly) regular upload processing if we're still errorless
if response_code == 200:
if upload_option == 'upload_file':
tool_params = upload_common.persist_uploads(tool_params, trans)
uploaded_datasets = upload_common.get_uploaded_datasets(trans, cntrller, tool_params, dataset_upload_inputs, library_bunch=library_bunch)
elif upload_option == 'upload_directory':
uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(trans, kwd, full_dir, import_dir_desc, library_bunch, response_code, message)
elif upload_option == 'upload_paths':
uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(trans, kwd, library_bunch, response_code, message)
if upload_option == 'upload_file' and not uploaded_datasets:
response_code = 400
message = 'Select a file, enter a URL or enter text'
if response_code != 200:
return (response_code, message)
json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
data_list = [ud.data for ud in uploaded_datasets]
job_params = {}
job_params['link_data_only'] = json.dumps(kwd.get('link_data_only', 'copy_files'))
job_params['uuid'] = json.dumps(kwd.get('uuid', None))
job, output = upload_common.create_job(trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params)
trans.sa_session.add(job)
trans.sa_session.flush()
return output
def check_src(item):
if "object_id" in item:
raise RequestParameterInvalidException(
"object_id not allowed to appear in the request.")
validate_datatype_extension(
datatypes_registry=trans.app.datatypes_registry,
ext=item.get('ext'))
# Normalize file:// URLs into paths.
if item["src"] == "url":
if "url" not in item:
raise RequestParameterInvalidException(
"src specified as 'url' but 'url' not specified")
url = item["url"]
if url.startswith("file://"):
item["src"] = "path"
item["path"] = url[len("file://"):]
del item["url"]
if "in_place" in item:
raise RequestParameterInvalidException(
"in_place cannot be set in the upload request")
src = item["src"]
# Check link_data_only can only be set for certain src types and certain elements_from types.
_handle_invalid_link_data_only_elements_type(item)
if src not in ["path", "server_dir"]:
_handle_invalid_link_data_only_type(item)
elements_from = item.get("elements_from", None)
if elements_from and elements_from not in ELEMENTS_FROM_TYPE:
raise RequestParameterInvalidException(
"Invalid elements_from/items_from found in request")
if src == "path" or (src == "url" and item["url"].startswith("file:")):
# Validate is admin, leave alone.
validate_path_upload(trans)
elif src == "server_dir":
# Validate and replace with path definition.
server_dir = item["server_dir"]
full_path, _ = validate_server_directory_upload(trans, server_dir)
item["src"] = "path"
item["path"] = full_path
elif src == "ftp_import":
ftp_path = item["ftp_path"]
full_path = None
# It'd be nice if this can be de-duplicated with what is in parameters/grouping.py.
user_ftp_dir = trans.user_ftp_dir
is_directory = False
assert not os.path.islink(
user_ftp_dir), "User FTP directory cannot be a symbolic link"
for (dirpath, dirnames, filenames) in os.walk(user_ftp_dir):
for filename in filenames:
if ftp_path == filename:
path = relpath(os.path.join(dirpath, filename),
user_ftp_dir)
if not os.path.islink(os.path.join(dirpath, filename)):
full_path = os.path.abspath(
os.path.join(user_ftp_dir, path))
break
for dirname in dirnames:
if ftp_path == dirname:
path = relpath(os.path.join(dirpath, dirname),
user_ftp_dir)
if not os.path.islink(os.path.join(dirpath, dirname)):
full_path = os.path.abspath(
os.path.join(user_ftp_dir, path))
is_directory = True
break
if is_directory:
# If the target is a directory - make sure no files under it are symbolic links
for (dirpath, dirnames, filenames) in os.walk(full_path):
for filename in filenames:
if ftp_path == filename:
path = relpath(os.path.join(dirpath, filename),
full_path)
if not os.path.islink(
os.path.join(dirpath, filename)):
full_path = False
break
for dirname in dirnames:
if ftp_path == dirname:
path = relpath(os.path.join(dirpath, filename),
full_path)
if not os.path.islink(
os.path.join(dirpath, filename)):
full_path = False
break
if not full_path:
raise RequestParameterInvalidException(
"Failed to find referenced ftp_path or symbolic link was enountered"
)
item["src"] = "path"
item["path"] = full_path
item["purge_source"] = purge_ftp_source
elif src == "url":
url = item["url"]
looks_like_url = False
for url_prefix in ["http://", "https://", "ftp://", "ftps://"]:
if url.startswith(url_prefix):
looks_like_url = True
break
if not looks_like_url and trans.app.file_sources.looks_like_uri(
url):
looks_like_url = True
if not looks_like_url:
raise RequestParameterInvalidException(
"Invalid URL [%s] found in src definition." % url)
validate_url(url, trans.app.config.fetch_url_allowlist_ips)
item["in_place"] = run_as_real_user
elif src == "files":
item["in_place"] = run_as_real_user
# Small disagreement with traditional uploads - we purge less by default since whether purging
# happens varies based on upload options in non-obvious ways.
# https://github.com/galaxyproject/galaxy/issues/5361
if "purge_source" not in item:
item["purge_source"] = False
