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
def check_src(item):
if "object_id" in item:
raise RequestParameterInvalidException("object_id not allowed to appear in the request.")
# Normalize file:// URLs into paths.
if item["src"] == "url" and item["url"].startswith("file://"):
item["src"] = "path"
item["path"] = item["url"][len("file://"):]
del item["path"]
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:
raise RequestParameterInvalidException("Invalid URL [%s] found in src definition." % url)
validate_url(url, trans.app.config.fetch_url_whitelist_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
