Merge branch 'release_23.2' into release_24.0

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

@@ -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

@@ -1,6 +1,5 @@
 import logging
 from typing import (
-    cast,
     List,
     NamedTuple,
     Optional,
@@ -26,6 +25,7 @@
 class RDMFilesSourceProperties(FilesSourceProperties):
     url: str
     token: str
+    public_name: str
 
 
 class RecordFilename(NamedTuple):
@@ -80,7 +80,9 @@ def get_files_in_record(
         """
         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.
@@ -138,22 +140,17 @@ 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)
 
     @property
     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 @@ def get_error_msg(details: str) -> str:
     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

@@ -135,7 +135,8 @@ def _create_entry(
         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 @@ def get_files_in_record(
         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": {
@@ -360,23 +363,26 @@ def _get_record_files_from_response(self, record_id: str, response: dict) -> Lis
                 )
         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:
                 family_name = tokens[0]
                 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

@@ -728,7 +728,8 @@ def update_workflow_from_raw_description(
             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: