Merge pull request #18027 from davelopez/24.0_fix_files_sources_error_handling (8f4968f0) · Commits · NDIP / Galaxy

lib/galaxy/files/sources/_pyfilesystem2.py

+24 −13

Original line number	Diff line number	Diff line
		@@ -12,9 +12,14 @@ from typing import (
		)

		import fs
		import fs.errors
		from fs.base import FS
		from typing_extensions import Unpack

		from galaxy.exceptions import (
		AuthenticationRequired,
		MessageException,
		)
		from . import (
		BaseFilesSource,
		FilesSourceOptions,
		@@ -42,7 +47,7 @@ class PyFilesystem2FilesSource(BaseFilesSource):

		def _list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
		"""Return dictionary of 'Directory's and 'File's."""

		try:
		with self._open_fs(user_context=user_context, opts=opts) as h:
		if recursive:
		res: List[Dict[str, Any]] = []
		@@ -55,6 +60,12 @@ class PyFilesystem2FilesSource(BaseFilesSource):
		res = h.scandir(path, namespaces=["details"])
		to_dict = functools.partial(self._resource_info_to_dict, path)
		return list(map(to_dict, res))
		except fs.errors.PermissionDenied as e:
		raise AuthenticationRequired(
		f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
		)
		except fs.errors.FSError as e:
		raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e

		def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
		with open(native_path, "wb") as write_file:

lib/galaxy/files/sources/dropbox.py

+15 −2

Original line number	Diff line number	Diff line
		@@ -8,6 +8,10 @@ from typing import (
		Union,
		)

		from galaxy.exceptions import (
		AuthenticationRequired,
		MessageException,
		)
		from . import (
		FilesSourceOptions,
		FilesSourceProperties,
		@@ -27,8 +31,17 @@ class DropboxFilesSource(PyFilesystem2FilesSource):
		if "accessToken" in props:
		props["access_token"] = props.pop("accessToken")

		try:
		handle = DropboxFS({props, **extra_props})
		return handle
		except Exception as e:
		# This plugin might raise dropbox.dropbox_client.BadInputException
		# which is not a subclass of fs.errors.FSError
		if "OAuth2" in str(e):
		raise AuthenticationRequired(
		f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
		)
		raise MessageException(f"Error connecting to Dropbox. Reason: {e}")


		__all__ = ("DropboxFilesSource",)

lib/galaxy/managers/remote_files.py

+9 −2

Original line number	Diff line number	Diff line
		@@ -9,6 +9,7 @@ from typing import (
		from galaxy import exceptions
		from galaxy.files import (
		ConfiguredFileSources,
		FileSourcePath,
		ProvidesUserFileSourcesUserContext,
		)
		from galaxy.files.sources import (
		@@ -94,10 +95,10 @@ class RemoteFilesManager:
		opts=opts,
		)
		except exceptions.MessageException:
		log.warning(f"Problem listing file source path {file_source_path}", exc_info=True)
		log.warning(self._get_error_message(file_source_path), exc_info=True)
		raise
		except Exception:
		message = f"Problem listing file source path {file_source_path}"
		message = self._get_error_message(file_source_path)
		log.warning(message, exc_info=True)
		raise exceptions.InternalServerError(message)
		if format == RemoteFilesFormat.flat:
		@@ -131,6 +132,9 @@ class RemoteFilesManager:

		return index

		def _get_error_message(self, file_source_path: FileSourcePath) -> str:
		return f"Problem listing file source path {file_source_path.file_source.get_uri_root()}{file_source_path.path}"

		def get_files_source_plugins(
		self,
		user_context: ProvidesUserContext,
		@@ -162,6 +166,9 @@ class RemoteFilesManager:
		file_source = file_source_path.file_source
		try:
		result = file_source.create_entry(entry_data.dict(), user_context=user_file_source_context)
		except exceptions.MessageException:
		log.warning(f"Problem creating entry {entry_data.name} in file source {entry_data.target}", exc_info=True)
		raise
		except Exception:
		message = f"Problem creating entry {entry_data.name} in file source {entry_data.target}"
		log.warning(message, exc_info=True)