Merge branch 'release_24.1' into dev

lib/galaxy/files/__init__.py

@@ -360,6 +360,9 @@ def user_vault(self) -> Dict[str, Any]: ...
     @property
     def app_vault(self) -> Dict[str, Any]: ...
 
+    @property
+    def anonymous(self) -> bool: ...
+
 
 OptionalUserContext = Optional[FileSourcesUserContext]
 
@@ -422,6 +425,10 @@ def app_vault(self):
     def file_sources(self):
         return self.trans.app.file_sources
 
+    @property
+    def anonymous(self) -> bool:
+        return self.trans.anonymous
+
 
 class DictFileSourcesUserContext(FileSourcesUserContext, FileSourceDictifiable):
     def __init__(self, **kwd):
@@ -466,3 +473,7 @@ def app_vault(self):
     @property
     def file_sources(self):
         return self._kwd.get("file_sources")
+
+    @property
+    def anonymous(self) -> bool:
+        return bool(self._kwd.get("username"))

lib/galaxy/managers/file_source_instances.py

@@ -483,6 +483,9 @@ def user_file_sources_to_dicts(
         exclude_kind: Optional[Set[PluginKind]] = None,
     ) -> List[FilesSourceProperties]:
         """Write out user file sources as list of config dictionaries."""
+        if user_context.anonymous:
+            return []
+
         as_dicts = []
         for files_source_properties in self._all_user_file_source_properties(user_context):
             plugin_kind = PluginKind.rfs

lib/galaxy/managers/jobs.py

@@ -1,13 +1,14 @@
 import json
 import logging
-import typing
 from datetime import (
     date,
     datetime,
 )
 from typing import (
     cast,
+    Dict,
     List,
+    Optional,
 )
 
 import sqlalchemy
@@ -38,6 +39,7 @@
     Safety,
 )
 from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.lddas import LDDAManager
@@ -106,7 +108,9 @@ def __init__(self, app: StructuredApp):
         self.app = app
         self.dataset_manager = DatasetManager(app)
 
-    def index_query(self, trans, payload: JobIndexQueryPayload) -> sqlalchemy.engine.Result:
+    def index_query(
+        self, trans: ProvidesUserContext, payload: JobIndexQueryPayload
+    ) -> Optional[sqlalchemy.engine.ScalarResult]:
         """The caller is responsible for security checks on the resulting job if
         history_id, invocation_id, or implicit_collection_jobs_id is set.
         Otherwise this will only return the user's jobs or all jobs if the requesting
@@ -122,6 +126,13 @@ def index_query(self, trans, payload: JobIndexQueryPayload) -> sqlalchemy.engine
         search = payload.search
         order_by = payload.order_by
 
+        if trans.user is None:
+            # If the user is anonymous we can only return jobs for the current session history
+            if trans.galaxy_session and trans.galaxy_session.current_history_id:
+                history_id = trans.galaxy_session.current_history_id
+            else:
+                return None
+
         def build_and_apply_filters(stmt, objects, filter_func):
             if objects is not None:
                 if isinstance(objects, (str, date, datetime)):
@@ -208,7 +219,7 @@ def add_search_criteria(stmt):
             if user_details:
                 stmt = stmt.outerjoin(Job.user)
         else:
-            if history_id is None and invocation_id is None and implicit_collection_jobs_id is None:
+            if history_id is None and invocation_id is None and implicit_collection_jobs_id is None and trans.user:
                 stmt = stmt.where(Job.user_id == trans.user.id)
             # caller better check security
 
@@ -647,7 +658,7 @@ def _build_stmt_for_dce(self, stmt, data_conditions, used_ids, k, v):
         return stmt
 
 
-def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
+def view_show_job(trans, job: Job, full: bool) -> Dict:
     is_admin = trans.user_is_admin
     job_dict = job.to_dict("element", system_details=is_admin)
     if trans.app.config.expose_dataset_path and "command_line" not in job_dict:

lib/galaxy/webapps/galaxy/services/jobs.py

@@ -81,7 +81,9 @@ def index(
             or payload.history_id is not None
         )
         jobs = self.job_manager.index_query(trans, payload)
-        out = []
+        out: List[Dict[str, Any]] = []
+        if jobs is None:
+            return out
         for job in jobs.yield_per(model.YIELD_PER_ROWS):
             # TODO: optimize if this crucial
             if check_security_of_jobs and not security_check(trans, job.history, check_accessible=True):

lib/galaxy/workflow/modules.py

@@ -131,9 +131,9 @@ def to_cwl(value, hda_references, step):
     element_identifier = None
     if isinstance(value, model.HistoryDatasetCollectionAssociation):
         value = value.collection
-    if isinstance(value, model.DatasetCollectionElement) and value.hda:
+    if isinstance(value, model.DatasetCollectionElement):
         element_identifier = value.element_identifier
-        value = value.hda
+        value = value.element_object
     if isinstance(value, model.HistoryDatasetAssociation):
         # I think the following two checks are needed but they may
         # not be needed.

test/unit/workflows/test_modules.py

@@ -274,6 +274,18 @@ def test_to_cwl_nested_collection():
     assert result["outer"][0]["basename"] == "inner"
 
 
+def test_to_cwl_dataset_collection_element():
+    hda = model.HistoryDatasetAssociation(create_dataset=True, flush=False)
+    hda.dataset.state = model.Dataset.states.OK
+    dc_inner = model.DatasetCollection(collection_type="list")
+    model.DatasetCollectionElement(collection=dc_inner, element_identifier="inner", element=hda)
+    dc_outer = model.DatasetCollection(collection_type="list:list")
+    dce_outer = model.DatasetCollectionElement(collection=dc_outer, element_identifier="outer", element=dc_inner)
+    result = modules.to_cwl(dce_outer, [], model.WorkflowStep())
+    assert result[0]["class"] == "File"
+    assert result[0]["basename"] == "inner"
+
+
 class MapOverTestCase(NamedTuple):
     data_input: str
     step_input_def: Union[str, List[str]]