Split raw_to_galaxy() trans requirement to app and history

Marginal improvement, but might be nice not to be bound to
`trans.history`.

Co-authored-by: Marius van den Beek <[email protected]>

lib/galaxy/tools/parameters/basic.py

@@ -65,7 +65,12 @@
 if TYPE_CHECKING:
     from sqlalchemy.orm import Session
 
+    from galaxy.model import (
+        History,
+        HistoryItem,
+    )
     from galaxy.security.idencoding import IdEncodingHelper
+    from galaxy.structured_app import MinimalApp
 
 log = logging.getLogger(__name__)
 
@@ -2116,7 +2121,7 @@ def from_json(self, value, trans, other_values=None):
             raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
         if value in [None, "None", ""]:
             if self.default_object:
-                return raw_to_galaxy(trans, self.default_object)
+                return raw_to_galaxy(trans.app, trans.history, self.default_object)
             return None
         if isinstance(value, MutableMapping) and "values" in value:
             value = self.to_python(value, trans.app)
@@ -2456,7 +2461,7 @@ def from_json(self, value, trans, other_values=None):
             raise ParameterValueError("specify a dataset collection of the correct type", self.name)
         if value in [None, "None"]:
             if self.default_object:
-                return raw_to_galaxy(trans, self.default_object)
+                return raw_to_galaxy(trans.app, trans.history, self.default_object)
             return None
         if isinstance(value, MutableMapping) and "values" in value:
             value = self.to_python(value, trans.app)
@@ -2672,10 +2677,7 @@ def to_text(self, value):
 
 # Code from CWL branch to massage in order to be shared across tools and workflows,
 # and for CWL artifacts as well as Galaxy ones.
-def raw_to_galaxy(trans, as_dict_value):
-    app = trans.app
-    history = trans.history
-
+def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any]) -> "HistoryItem":
     object_class = as_dict_value["class"]
     if object_class == "File":
         # TODO: relative_to = "/"
@@ -2714,15 +2716,15 @@ def raw_to_galaxy(trans, as_dict_value):
             dbkey="?",
             dataset=dataset,
             flush=False,
-            sa_session=trans.sa_session,
+            sa_session=app.model.session,
         )
         primary_data.state = Dataset.states.DEFERRED
         permissions = app.security_agent.history_get_default_permissions(history)
         app.security_agent.set_all_dataset_permissions(primary_data.dataset, permissions, new=True, flush=False)
-        trans.sa_session.add(primary_data)
+        app.model.session.add(primary_data)
         history.stage_addition(primary_data)
         history.add_pending_items()
-        trans.sa_session.flush()
+        app.model.session.flush()
         return primary_data
     else:
         name = as_dict_value.get("name")
@@ -2741,7 +2743,7 @@ def write_elements_to_collection(has_elements, collection_builder):
                 element_class = element_dict["class"]
                 identifier = element_dict["identifier"]
                 if element_class == "File":
-                    hda = raw_to_galaxy(trans, element_dict)
+                    hda = raw_to_galaxy(app, history, element_dict)
                     collection_builder.add_dataset(identifier, hda)
                 else:
                     subcollection_builder = collection_builder.get_level(identifier)
@@ -2750,8 +2752,8 @@ def write_elements_to_collection(has_elements, collection_builder):
         collection_builder = builder.BoundCollectionBuilder(collection)
         write_elements_to_collection(as_dict_value, collection_builder)
         collection_builder.populate()
-        trans.sa_session.add(hdca)
-        trans.sa_session.flush()
+        app.model.session.add(hdca)
+        app.model.session.flush()
         return hdca
 
 

lib/galaxy/workflow/modules.py

@@ -942,7 +942,7 @@ def execute(
         if input_value is None:
             default_value = step.get_input_default_value(NO_REPLACEMENT)
             if default_value is not NO_REPLACEMENT:
-                input_value = raw_to_galaxy(trans, default_value)
+                input_value = raw_to_galaxy(trans.app, trans.history, default_value)
 
         step_outputs = dict(output=input_value)
 

lib/galaxy/workflow/run.py

@@ -45,6 +45,7 @@
 
 if TYPE_CHECKING:
     from galaxy.model import (
+        HistoryItem,
         Workflow,
         WorkflowOutput,
         WorkflowStep,
@@ -422,6 +423,7 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
             modules.NoReplacement,
             model.DatasetCollectionInstance,
             List[model.DatasetCollectionInstance],
+            "HistoryItem",
         ] = modules.NO_REPLACEMENT
         prefixed_name = input_dict["name"]
         multiple = input_dict["multiple"]
@@ -446,7 +448,7 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
             for step_input in step.inputs:
                 if step_input.name == prefixed_name and step_input.default_value_set:
                     if is_data:
-                        replacement = raw_to_galaxy(trans, step_input.default_value)
+                        replacement = raw_to_galaxy(trans.app, trans.history, step_input.default_value)
         return replacement
 
     def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True):
@@ -713,7 +715,7 @@ def subworkflow_progress(
         )
 
     def raw_to_galaxy(self, value: dict):
-        return raw_to_galaxy(self.module_injector.trans, value)
+        return raw_to_galaxy(self.module_injector.trans.app, self.module_injector.trans.history, value)
 
     def _recover_mapping(self, step_invocation: WorkflowInvocationStep) -> None:
         try: