Allow recovering a normalized version of workflow request state from API

.github/workflows/framework_workflows.yaml

@@ -16,6 +16,7 @@ on:
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_WORKFLOW_AFTER_RERUN: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

client/src/api/schema/schema.ts

@@ -2645,6 +2645,23 @@ export interface paths {
         patch?: never;
         trace?: never;
     };
+    "/api/invocations/{invocation_id}/request": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get a description modeling an API request to invoke this workflow - this is recreated and will be more specific in some ways than the initial creation request. */
+        get: operations["invocation_as_request_api_invocations__invocation_id__request_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/invocations/{invocation_id}/step_jobs_summary": {
         parameters: {
             query?: never;
@@ -12385,8 +12402,9 @@ export interface components {
              */
             batch: boolean | null;
             /**
-             * Dataset Map
-             * @description TODO
+             * Legacy Dataset Map
+             * @deprecated
+             * @description An older alternative to specifying inputs using database IDs, do not use this and use inputs instead
              * @default {}
              */
             ds_map: {
@@ -12409,12 +12427,12 @@ export interface components {
             history_id?: string | null;
             /**
              * Inputs
-             * @description TODO
+             * @description Specify values for formal inputs to the workflow
              */
             inputs?: Record<string, never> | null;
             /**
              * Inputs By
-             * @description How inputs maps to inputs (datasets/collections) to workflows steps.
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
              */
             inputs_by?: string | null;
             /**
@@ -12441,35 +12459,35 @@ export interface components {
              */
             no_add_to_history: boolean | null;
             /**
-             * Parameters
-             * @description The raw parameters for the workflow invocation.
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead.
              * @default {}
              */
             parameters: Record<string, never> | null;
             /**
-             * Parameters Normalized
-             * @description Indicates if parameters are already normalized for workflow invocation.
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
              * @default false
              */
             parameters_normalized: boolean | null;
             /**
              * Preferred Intermediate Object Store ID
-             * @description The ID of the ? object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_intermediate_object_store_id?: string | null;
             /**
              * Preferred Object Store ID
-             * @description The ID of the object store that should be used to store new datasets in this history.
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_object_store_id?: string | null;
             /**
              * Preferred Outputs Object Store ID
-             * @description The ID of the object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
              */
             preferred_outputs_object_store_id?: string | null;
             /**
              * Replacement Parameters
-             * @description TODO
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
              * @default {}
              */
             replacement_params: Record<string, never> | null;
@@ -12481,7 +12499,7 @@ export interface components {
             require_exact_tool_versions: boolean | null;
             /**
              * Resource Parameters
-             * @description TODO
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
              * @default {}
              */
             resource_params: Record<string, never> | null;
@@ -12490,11 +12508,6 @@ export interface components {
              * @description Scheduler to use for workflow invocation.
              */
             scheduler?: string | null;
-            /**
-             * Step Parameters
-             * @description TODO
-             */
-            step_parameters?: Record<string, never> | null;
             /**
              * Use cached job
              * @description Indicated whether to use a cached job for workflow invocation.
@@ -18188,6 +18201,86 @@ export interface components {
              */
             workflow_id: string;
         };
+        /**
+         * WorkflowInvocationRequestModel
+         * @description Model a workflow invocation request (InvokeWorkflowPayload) for an existing invocation.
+         */
+        WorkflowInvocationRequestModel: {
+            /**
+             * History ID
+             * @description The encoded history id the workflow was run in.
+             */
+            history_id: string;
+            /**
+             * Inputs
+             * @description Values for inputs
+             */
+            inputs: Record<string, never>;
+            /**
+             * Inputs by
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
+             */
+            inputs_by: string;
+            /**
+             * Is instance
+             * @description This API yields a particular workflow instance, newer workflows belonging to the same storedworkflow may have different state.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            instance: true;
+            /**
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead. If these are set, the workflow was not executed in a best-practice fashion and we the resulting invocation request may not fully reflect the executed workflow state.
+             */
+            parameters?: Record<string, never> | null;
+            /**
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            parameters_normalized: true;
+            /**
+             * Preferred Intermediate Object Store ID
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_intermediate_object_store_id?: string | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Preferred Outputs Object Store ID
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
+             */
+            preferred_outputs_object_store_id?: string | null;
+            /**
+             * Replacement Parameters
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
+             * @default {}
+             */
+            replacement_params: Record<string, never> | null;
+            /**
+             * Resource Parameters
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
+             * @default {}
+             */
+            resource_params: Record<string, never> | null;
+            /**
+             * Use cached job
+             * @description Indicated whether to use a cached job for workflow invocation.
+             * @default false
+             */
+            use_cached_job: boolean;
+            /**
+             * Workflow ID
+             * @description The encoded Workflow ID associated with the invocation.
+             */
+            workflow_id: string;
+        };
         /** WorkflowInvocationResponse */
         WorkflowInvocationResponse:
             | components["schemas"]["WorkflowInvocationElementView"]
@@ -27056,6 +27149,50 @@ export interface operations {
             };
         };
     };
+    invocation_as_request_api_invocations__invocation_id__request_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["WorkflowInvocationRequestModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
     invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get: {
         parameters: {
             query?: never;

lib/galaxy/model/__init__.py

@@ -7749,6 +7749,16 @@ def get_internal_version(self, version):
             raise galaxy.exceptions.RequestParameterInvalidException("Version does not exist")
         return list(reversed(self.workflows))[version]
 
+    def get_internal_version_by_id(self, workflow_instance_id: int):
+        sa_session = object_session(self)
+        assert sa_session
+        workflow = sa_session.get(Workflow, workflow_instance_id)
+        if not workflow:
+            raise galaxy.exceptions.ObjectNotFound()
+        elif workflow.stored_workflow != self:
+            raise galaxy.exceptions.RequestParameterInvalidException()
+        return workflow
+
     def version_of(self, workflow):
         for version, workflow_instance in enumerate(reversed(self.workflows)):
             if workflow_instance.id == workflow.id:
@@ -8015,7 +8025,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
     type: Mapped[Optional[str]] = mapped_column(String(64))
     tool_id: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_version: Mapped[Optional[str]] = mapped_column(TEXT)
-    tool_inputs: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    tool_inputs: Mapped[Optional[Dict[str, Any]]] = mapped_column(JSONType)
     tool_errors: Mapped[Optional[bytes]] = mapped_column(JSONType)
     position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     config: Mapped[Optional[bytes]] = mapped_column(JSONType)
@@ -8085,11 +8095,13 @@ def init_on_load(self):
     def tool_uuid(self):
         return self.dynamic_tool and self.dynamic_tool.uuid
 
+    @property
+    def is_input_type(self) -> bool:
+        return bool(self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE)
+
     @property
     def input_type(self):
-        assert (
-            self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE
-        ), "step.input_type can only be called on input step types"
+        assert self.is_input_type, "step.input_type can only be called on input step types"
         return self.STEP_TYPE_TO_INPUT_TYPE[self.type]
 
     @property
@@ -8310,6 +8322,17 @@ def log_str(self):
             f"WorkflowStep[index={self.order_index},type={self.type},label={self.label},uuid={self.uuid},id={self.id}]"
         )
 
+    @property
+    def effective_label(self) -> Optional[str]:
+        label = self.label
+        if label is not None:
+            return label
+        elif self.is_input_type:
+            tool_inputs = self.tool_inputs
+            if tool_inputs is not None:
+                return cast(Optional[str], tool_inputs.get("name"))
+        return None
+
     def clear_module_extras(self):
         # the module code adds random dynamic state to the step, this
         # attempts to clear that.
@@ -9112,6 +9135,50 @@ def attach_step(request_to_content):
             attach_step(request_to_content)
             self.input_step_parameters.append(request_to_content)
 
+    def recover_inputs(self) -> Tuple[Dict[str, Any], str]:
+        inputs = {}
+        inputs_by = "name"
+
+        have_referenced_steps_by_order_index = False
+
+        def best_step_reference(workflow_step: "WorkflowStep") -> str:
+            label = workflow_step.effective_label
+            if label is not None:
+                return label
+            nonlocal have_referenced_steps_by_order_index
+            have_referenced_steps_by_order_index = True
+            return str(workflow_step.order_index)
+
+        def ensure_step(step: Optional["WorkflowStep"]) -> "WorkflowStep":
+            if step is None:
+                raise galaxy.exceptions.InconsistentDatabase(
+                    "workflow input found without step definition, this should not happen"
+                )
+            assert step
+            return step
+
+        for input_dataset_assoc in self.input_datasets:
+            workflow_step = ensure_step(input_dataset_assoc.workflow_step)
+            input_dataset = input_dataset_assoc.dataset
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = input_dataset
+
+        for input_dataset_collection_assoc in self.input_dataset_collections:
+            workflow_step = ensure_step(input_dataset_collection_assoc.workflow_step)
+            input_dataset_collection = input_dataset_collection_assoc.dataset_collection
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = input_dataset_collection
+
+        for input_step_parameter_assoc in self.input_step_parameters:
+            workflow_step = ensure_step(input_step_parameter_assoc.workflow_step)
+            value = input_step_parameter_assoc.parameter_value
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = value
+
+        if have_referenced_steps_by_order_index:
+            inputs_by = "name|step_index"
+        return inputs, inputs_by
+
     def add_message(self, message: "InvocationMessageUnion"):
         self.messages.append(
             WorkflowInvocationMessage(  # type:ignore[abstract]