Implement {src: "url"} on the new request API...

jmchilton · Sep 10, 2024 · 3dad4c7 · 3dad4c7
1 parent a563c0f
commit 3dad4c7
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Showing 22 changed files with 600 additions and 109 deletions.
diff --git a/doc/source/dev/tool_state_state_classes.plantuml.svg b/doc/source/dev/tool_state_state_classes.plantuml.svg
diff --git a/doc/source/dev/tool_state_state_classes.plantuml.txt b/doc/source/dev/tool_state_state_classes.plantuml.txt
@@ -6,36 +6,45 @@ package galaxy.tool_util.parameters.state {
 class ToolState {
 state_representation: str
 input_state: Dict[str, Any]
-+ validate(input_models: ToolParameterBundle)
-+ {abstract} _to_base_model(input_models: ToolParameterBundle): Optional[Type[BaseModel]]
++ validate(parameters: ToolParameterBundle)
++ {abstract} _to_base_model(parameters: ToolParameterBundle): Optional[Type[BaseModel]]
 }
 
 class RequestToolState {
 state_representation = "request"
-+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
 }
 note bottom: Object references of the form \n{src: "hda", id: <encoded_id>}.\n Allow mapping/reduce constructs.
 
 class RequestInternalToolState {
 state_representation = "request_internal"
-+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
 }
-note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs.
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. Allows URI src dicts.
+
+class RequestInternalDereferencedToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. No URI src dicts - all converted to HDAs.
 
 class JobInternalToolState {
 state_representation = "job_internal"
-+ _to_base_model(input_models: ToolParameterBundle): Type[BaseModel]
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
 
 }
 note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Mapping constructs expanded out.\n (Defaults are inserted?)
 
 ToolState <|-- RequestToolState
 ToolState <|-- RequestInternalToolState
+ToolState <|-- RequestInternalDereferencedToolState
 ToolState <|-- JobInternalToolState
 
 RequestToolState - RequestInternalToolState : decode >
 
-RequestInternalToolState o-- JobInternalToolState : expand >
+RequestInternalToolState - RequestInternalDereferencedToolState : dereference > 
+
+RequestInternalDereferencedToolState o-- JobInternalToolState : expand >
 
 }
 @enduml
diff --git a/doc/source/dev/tool_state_task.plantuml.svg b/doc/source/dev/tool_state_task.plantuml.svg
diff --git a/doc/source/dev/tool_state_task.plantuml.txt b/doc/source/dev/tool_state_task.plantuml.txt
@@ -0,0 +1,25 @@
+@startuml
+'!include plantuml_options.txt
+queue       TaskQueue   as queue
+participant     "queue_jobs Task" as task
+participant     "JobSubmitter.queue_jobs" as queue_jobs
+participant     "JobSubmitter.dereference" as dereference
+participant     "materialize Task" as materialize_task
+participant     "Tool.handle_input_async" as handle_input
+participant     "expand_meta_parameters_async" as expand
+participant     "ToolAction.execute" as tool_action
+
+queue -> task : <Launch Task>
+task -> queue_jobs : QueueJobs pydantic model
+queue_jobs -> dereference : RequestInternalToolState
+dereference -> queue_jobs : RequestInternalDereferencedToolState
+queue_jobs -> materialize_task : HDA (with state deferred)
+materialize_task -> queue_jobs : return when state is okay
+queue_jobs -> handle_input : RequestInternalDereferencedToolState
+handle_input -> expand : RequestInternalDereferencedToolState
+expand -> handle_input : JobInternalToolState[]
+loop over expanded job tool states
+    handle_input -> tool_action :
+    tool_action -> handle_input : A Galaxy Job
+end
+@enduml
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
@@ -173,7 +173,7 @@ def create(
                 session.commit()
         return hda
 
-    def materialize(self, request: MaterializeDatasetInstanceTaskRequest) -> None:
+    def materialize(self, request: MaterializeDatasetInstanceTaskRequest, in_place: bool = False) -> None:
         request_user: RequestUser = request.user
         materializer = materializer_factory(
             True,  # attached...
@@ -187,8 +187,9 @@ def materialize(self, request: MaterializeDatasetInstanceTaskRequest) -> None:
         else:
             dataset_instance = self.ldda_manager.get_accessible(request.content, user)
         history = self.app.history_manager.by_id(request.history_id)
-        new_hda = materializer.ensure_materialized(dataset_instance, target_history=history)
-        history.add_dataset(new_hda, set_hid=True)
+        new_hda = materializer.ensure_materialized(dataset_instance, target_history=history, in_place=in_place)
+        if not in_place:
+            history.add_dataset(new_hda, set_hid=True)
         session = self.session()
         with transaction(session):
             session.commit()