Merge branch 'release_23.2' into release_24.0 (33538bea) · Commits · NDIP / Galaxy

lib/galaxy/config/sample/file_sources_conf.yml.sample

+7 −3

Original line number	Diff line number	Diff line
		@@ -202,10 +202,14 @@
		doc: Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.

		- type: inveniordm
		id: invenio
		doc: Invenio RDM turn-key research data management repository
		label: Invenio RDM Demo Repository
		id: invenio_sandbox
		doc: This is the Sandbox instance of Invenio. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.
		label: Invenio RDM Sandbox Repository (TESTING ONLY)
		url: https://inveniordm.web.cern.ch/
		token: ${user.user_vault.read_secret('preferences/invenio_sandbox/token')}
		# token: ${user.preferences['invenio_sandbox\|token']} # Alternatively use this for retrieving the token from user preferences instead of the Vault
		public_name: ${user.preferences['invenio_sandbox\|public_name']}
		writable: true

		- type: onedata
		id: onedata1

lib/galaxy/files/sources/_rdm.py

+18 −23

Original line number	Diff line number	Diff line
		import logging
		from typing import (
		cast,
		List,
		NamedTuple,
		Optional,
		@@ -26,6 +25,7 @@ OptionalUserContext = Optional[ProvidesUserFileSourcesUserContext]
		class RDMFilesSourceProperties(FilesSourceProperties):
		url: str
		token: str
		public_name: str


		class RecordFilename(NamedTuple):
		@@ -80,7 +80,9 @@ class RDMRepositoryInteractor:
		"""
		raise NotImplementedError()

		def create_draft_record(self, title: str, user_context: OptionalUserContext = None):
		def create_draft_record(
		self, title: str, public_name: Optional[str] = None, user_context: OptionalUserContext = None
		):
		"""Creates a draft record (directory) in the repository with basic metadata.

		The metadata is usually just the title of the record and the user that created it.
		@@ -138,11 +140,10 @@ class RDMFilesSource(BaseFilesSource):

		def __init__(self, **kwd: Unpack[FilesSourceProperties]):
		props = self._parse_common_config_opts(kwd)
		base_url = props.get("url", None)
		base_url = props.get("url")
		if not base_url:
		raise Exception("URL for RDM repository must be provided in configuration")
		self._repository_url = base_url
		self._token = props.get("token", None)
		self._props = props
		self._repository_interactor = self.get_repository_interactor(base_url)

		@@ -150,10 +151,6 @@ class RDMFilesSource(BaseFilesSource):
		def repository(self) -> RDMRepositoryInteractor:
		return self._repository_interactor

		@property
		def token(self) -> Optional[str]:
		return self._token if self._token and not self._token.startswith("$") else None

		def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInteractor:
		"""Returns an interactor compatible with the given repository URL.

		@@ -190,25 +187,23 @@ class RDMFilesSource(BaseFilesSource):
		def get_record_id_from_path(self, source_path: str) -> str:
		return self.parse_path(source_path, record_id_only=True).record_id

		def _serialization_props(self, user_context: OptionalUserContext = None) -> RDMFilesSourceProperties:
		def _serialization_props(self, user_context: OptionalUserContext = None):
		effective_props = {}
		for key, val in self._props.items():
		effective_props[key] = self._evaluate_prop(val, user_context=user_context)
		effective_props["url"] = self._repository_url
		effective_props["token"] = self.safe_get_authorization_token(user_context)
		return cast(RDMFilesSourceProperties, effective_props)
		return effective_props

		def get_authorization_token(self, user_context: OptionalUserContext) -> str:
		token = self.token
		if not token and user_context:
		vault = user_context.user_vault if user_context else None
		token = vault.read_secret(f"preferences/{self.id}/token") if vault else None
		if token is None:
		raise AuthenticationRequired(f"No authorization token provided in user's settings for '{self.label}'")
		token = None
		if user_context:
		effective_props = self._serialization_props(user_context)
		token = effective_props.get("token")
		if not token:
		raise AuthenticationRequired(
		f"Please provide a personal access token in your user's preferences for '{self.label}'"
		)
		return token

		def safe_get_authorization_token(self, user_context: OptionalUserContext) -> Optional[str]:
		try:
		return self.get_authorization_token(user_context)
		except AuthenticationRequired:
		return None
		def get_public_name(self, user_context: OptionalUserContext) -> Optional[str]:
		effective_props = self._serialization_props(user_context)
		return effective_props.get("public_name")

lib/galaxy/files/sources/invenio.py

+18 −12

Original line number	Diff line number	Diff line
		@@ -135,7 +135,8 @@ class InvenioRDMFilesSource(RDMFilesSource):
		user_context: OptionalUserContext = None,
		opts: Optional[FilesSourceOptions] = None,
		) -> Entry:
		record = self.repository.create_draft_record(entry_data["name"], user_context=user_context)
		public_name = self.get_public_name(user_context)
		record = self.repository.create_draft_record(entry_data["name"], public_name, user_context=user_context)
		return {
		"uri": self.repository.to_plugin_uri(record["id"]),
		"name": record["metadata"]["title"],
		@@ -198,9 +199,11 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
		response_data = self._get_response(user_context, request_url)
		return self._get_record_files_from_response(record_id, response_data)

		def create_draft_record(self, title: str, user_context: OptionalUserContext = None) -> RemoteDirectory:
		def create_draft_record(
		self, title: str, public_name: Optional[str] = None, user_context: OptionalUserContext = None
		) -> RemoteDirectory:
		today = datetime.date.today().isoformat()
		creator = self._get_creator_from_user_context(user_context)
		creator = self._get_creator_from_public_name(public_name)
		create_record_request = {
		"files": {"enabled": True},
		"metadata": {
		@@ -360,10 +363,9 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
		)
		return rval

		def _get_creator_from_user_context(self, user_context: OptionalUserContext):
		public_name = self.get_user_preference_by_key("public_name", user_context)
		family_name = "Galaxy User"
		def _get_creator_from_public_name(self, public_name: Optional[str] = None) -> Creator:
		given_name = "Anonymous"
		family_name = "Galaxy User"
		if public_name:
		tokens = public_name.split(", ")
		if len(tokens) == 2:
		@@ -371,12 +373,16 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
		given_name = tokens[1]
		else:
		given_name = public_name
		return {"person_or_org": {"family_name": family_name, "given_name": given_name, "type": "personal"}}

		def get_user_preference_by_key(self, key: str, user_context: OptionalUserContext):
		preferences = user_context.preferences if user_context else None
		value = preferences.get(f"{self.plugin.id}\|{key}", None) if preferences else None
		return value
		return {
		"person_or_org": {
		"name": f"{given_name} {family_name}",
		"family_name": family_name,
		"given_name": given_name,
		"type": "personal",
		"identifiers": [],
		},
		"affiliations": [],
		}

		def _get_response(
		self, user_context: OptionalUserContext, request_url: str, params: Optional[Dict[str, Any]] = None

lib/galaxy/managers/workflows.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -728,7 +728,8 @@ class WorkflowContentsManager(UsesAnnotations):
		trans.tag_handler.set_tags_from_list(
		trans.user,
		stored_workflow,
		data.get("tags", []),
		data["tags"],
		flush=False,
		)

		if workflow_update_options.update_stored_workflow_attributes:

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