Merge branch 'release_24.0' into release_24.1 (49660628) · Commits · NDIP / Galaxy

lib/galaxy/managers/citations.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -152,7 +152,7 @@ class DoiCitation(BaseCitation):
		try:
		self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi)
		except Exception:
		log.exception("Failed to fetch bibtex for DOI %s", self.__doi)
		log.debug("Failed to fetch bibtex for DOI %s", self.__doi)

		if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
		return f"""@MISC{{{self.__doi},

lib/galaxy/schema/schema.py

+3 −0

Original line number	Diff line number	Diff line
		@@ -349,6 +349,9 @@ class LimitedUserModel(Model):
		email: Optional[str] = None


		MaybeLimitedUserModel = Union[UserModel, LimitedUserModel]


		class DiskUsageUserModel(Model):
		total_disk_usage: float = TotalDiskUsageField
		nice_total_disk_usage: str = NiceTotalDiskUsageField

lib/galaxy/webapps/base/webapp.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -949,6 +949,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
		self.set_history(history)
		return history

		# Don't create new history if login required and user is anonymous
		if self.app.config.require_login and not self.user:
		return None

		# No suitable history found, create a new one.
		return self.new_history()

lib/galaxy/webapps/galaxy/api/users.py

+3 −4

Original line number	Diff line number	Diff line
		@@ -56,12 +56,11 @@ from galaxy.schema.schema import (
		FavoriteObjectsSummary,
		FavoriteObjectType,
		FlexibleUserIdType,
		LimitedUserModel,
		MaybeLimitedUserModel,
		RemoteUserCreationPayload,
		UserBeaconSetting,
		UserCreationPayload,
		UserDeletionPayload,
		UserModel,
		)
		from galaxy.security.validate_user_input import (
		validate_email,
		@@ -203,7 +202,7 @@ class FastAPIUsers:
		f_email: Optional[str] = FilterEmailQueryParam,
		f_name: Optional[str] = FilterNameQueryParam,
		f_any: Optional[str] = FilterAnyQueryParam,
		) -> List[Union[UserModel, LimitedUserModel]]:
		) -> List[MaybeLimitedUserModel]:
		return self.service.get_index(trans=trans, deleted=True, f_email=f_email, f_name=f_name, f_any=f_any)

		@router.post(
		@@ -651,7 +650,7 @@ class FastAPIUsers:
		f_email: Optional[str] = FilterEmailQueryParam,
		f_name: Optional[str] = FilterNameQueryParam,
		f_any: Optional[str] = FilterAnyQueryParam,
		) -> List[Union[UserModel, LimitedUserModel]]:
		) -> List[MaybeLimitedUserModel]:
		return self.service.get_index(trans=trans, deleted=deleted, f_email=f_email, f_name=f_name, f_any=f_any)

		@router.get(

lib/galaxy/webapps/galaxy/services/users.py

+12 −11

Original line number	Diff line number	Diff line
		@@ -35,6 +35,7 @@ from galaxy.schema.schema import (
		DetailedUserModel,
		FlexibleUserIdType,
		LimitedUserModel,
		MaybeLimitedUserModel,
		UserModel,
		)
		from galaxy.security.idencoding import IdEncodingHelper
		@@ -204,8 +205,8 @@ class UsersService(ServiceBase):
		f_email: Optional[str],
		f_name: Optional[str],
		f_any: Optional[str],
		) -> List[Union[UserModel, LimitedUserModel]]:
		rval = []
		) -> List[MaybeLimitedUserModel]:
		rval: List[MaybeLimitedUserModel] = []
		stmt = select(User)

		if f_email and (trans.user_is_admin or trans.app.config.expose_user_email):
		@@ -240,13 +241,12 @@ class UsersService(ServiceBase):
		and not trans.app.config.expose_user_email
		):
		if trans.user:
		item = trans.user.to_dict()
		return [item]
		return [UserModel(**trans.user.to_dict())]
		else:
		return []
		stmt = stmt.filter(User.deleted == false())
		for user in trans.sa_session.scalars(stmt).all():
		item = user.to_dict()
		user_dict = user.to_dict()
		# If NOT configured to expose_email, do not expose email UNLESS the user is self, or
		# the user is an admin
		if user is not trans.user and not trans.user_is_admin:
		@@ -255,12 +255,13 @@ class UsersService(ServiceBase):
		expose_keys.append("username")
		if trans.app.config.expose_user_email:
		expose_keys.append("email")
		new_item = {}
		for key, value in item.items():
		limited_user = {}
		for key, value in user_dict.items():
		if key in expose_keys:
		new_item[key] = value
		item = new_item
		limited_user[key] = value
		user = LimitedUserModel(**limited_user)
		else:
		user = UserModel(**user_dict)

		# TODO: move into api_values
		rval.append(item)
		rval.append(user)
		return rval

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