Merge branch 'release_24.1' into dev

client/src/components/Workflow/Editor/Actions/actions.test.ts

@@ -14,9 +14,10 @@ import {
     LazyChangeDataAction,
     LazyChangePositionAction,
     LazyChangeSizeAction,
+    RemoveAllFreehandCommentsAction,
     ToggleCommentSelectedAction,
 } from "./commentActions";
-import { mockComment, mockToolStep, mockWorkflow } from "./mockData";
+import { mockComment, mockFreehandComment, mockToolStep, mockWorkflow } from "./mockData";
 import {
     CopyStepAction,
     InsertStepAction,
@@ -90,6 +91,12 @@ describe("Workflow Undo Redo Actions", () => {
         return comment;
     }
 
+    function addFreehandComment() {
+        const comment = mockFreehandComment(commentStore.highestCommentId + 1);
+        commentStore.addComments([comment]);
+        return comment;
+    }
+
     function addStep() {
         const step = mockToolStep(stepStore.getStepIndex + 1);
         stepStore.addStep(step);
@@ -141,6 +148,15 @@ describe("Workflow Undo Redo Actions", () => {
             const action = new ToggleCommentSelectedAction(commentStore, comment);
             testUndoRedo(action);
         });
+
+        it("RemoveAllFreehandCommentsAction", () => {
+            addFreehandComment();
+            addFreehandComment();
+            addFreehandComment();
+
+            const action = new RemoveAllFreehandCommentsAction(commentStore);
+            testUndoRedo(action);
+        });
     });
 
     describe("Workflow Actions", () => {

client/src/components/Workflow/Editor/Actions/commentActions.ts

@@ -177,3 +177,28 @@ export class ToggleCommentSelectedAction extends UndoRedoAction {
         this.store.setCommentMultiSelected(this.commentId, !this.toggleTo);
     }
 }
+
+export class RemoveAllFreehandCommentsAction extends UndoRedoAction {
+    store;
+    comments;
+
+    constructor(store: WorkflowCommentStore) {
+        super();
+
+        this.store = store;
+        const freehandComments = store.comments.filter((comment) => comment.type === "freehand");
+        this.comments = structuredClone(freehandComments);
+    }
+
+    get name() {
+        return "remove all freehand comments";
+    }
+
+    run() {
+        this.store.deleteFreehandComments();
+    }
+
+    undo() {
+        this.store.addComments(structuredClone(this.comments));
+    }
+}

client/src/components/Workflow/Editor/Actions/mockData.ts

@@ -1,4 +1,4 @@
-import { WorkflowComment } from "@/stores/workflowEditorCommentStore";
+import { FreehandWorkflowComment, WorkflowComment } from "@/stores/workflowEditorCommentStore";
 import type { Step } from "@/stores/workflowStepStore";
 
 import type { Workflow } from "../modules/model";
@@ -227,3 +227,21 @@ export function mockComment(id: number): WorkflowComment {
         data: { size: 2, text: "Enter Text" },
     };
 }
+
+export function mockFreehandComment(id: number): FreehandWorkflowComment {
+    return {
+        id,
+        position: [0, 0],
+        size: [100, 200],
+        type: "freehand",
+        color: "none",
+        data: {
+            thickness: 1,
+            line: [
+                [0, 0],
+                [10, 20],
+                [100, 200],
+            ],
+        },
+    };
+}

client/src/components/Workflow/Editor/Tools/ToolBar.vue

@@ -21,6 +21,7 @@ import { BoxSelect } from "lucide-vue";
 import { storeToRefs } from "pinia";
 import { computed, toRefs, watch } from "vue";
 
+import { RemoveAllFreehandCommentsAction } from "@/components/Workflow/Editor/Actions/commentActions";
 import { useUid } from "@/composables/utils/uid";
 import { useWorkflowStores } from "@/composables/workflowStores";
 import { type CommentTool } from "@/stores/workflowEditorToolbarStore";
@@ -45,7 +46,7 @@ library.add(
     faTrash
 );
 
-const { toolbarStore, commentStore } = useWorkflowStores();
+const { toolbarStore, undoRedoStore, commentStore } = useWorkflowStores();
 const { snapActive, currentTool } = toRefs(toolbarStore);
 
 const { commentOptions } = toolbarStore;
@@ -122,7 +123,7 @@ const thicknessId = useUid("thickness-");
 const smoothingId = useUid("smoothing-");
 
 function onRemoveAllFreehand() {
-    commentStore.deleteFreehandComments();
+    undoRedoStore.applyAction(new RemoveAllFreehandCommentsAction(commentStore));
 }
 
 useToolLogic();

lib/galaxy/managers/datasets.py

@@ -489,12 +489,16 @@ class DatasetAssociationManager(
 
     def ensure_dataset_on_disk(self, trans, dataset):
         # Not a guarantee data is really present, but excludes a lot of expected cases
+        if not dataset.dataset:
+            raise exceptions.InternalServerError("Item has no associated dataset.")
         if dataset.purged or dataset.dataset.purged:
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been purged.")
         elif dataset.deleted and not (trans.user_is_admin or self.is_owner(dataset, trans.get_user())):
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been deleted.")
         elif dataset.state == Dataset.states.UPLOAD:
             raise exceptions.Conflict("Please wait until this dataset finishes uploading before attempting to view it.")
+        elif dataset.state == Dataset.states.NEW:
+            raise exceptions.Conflict("The dataset you are attempting to view is new and has no data.")
         elif dataset.state == Dataset.states.DISCARDED:
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been discarded.")
         elif dataset.state == Dataset.states.DEFERRED:

lib/galaxy/model/unittest_utils/data_app.py

@@ -61,6 +61,7 @@ class GalaxyDataTestConfig(Bunch):
         self.object_store = "disk"
         self.object_store_check_old_style = False
         self.object_store_cache_path = "/tmp/cache"
+        self.object_store_cache_size = -1
         self.object_store_store_by = "uuid"
 
         self.umask = os.umask(0o77)

lib/galaxy/objectstore/__init__.py

@@ -1726,6 +1726,7 @@ def config_to_dict(config):
         "jobs_directory": config.jobs_directory,
         "new_file_path": config.new_file_path,
         "object_store_cache_path": config.object_store_cache_path,
+        "object_store_cache_size": config.object_store_cache_size,
         "gid": config.gid,
     }
 

lib/galaxy/tools/parameters/wrapped.py

@@ -3,6 +3,8 @@ from typing import (
     Any,
     Dict,
     List,
+    Sequence,
+    Union,
 )
 
 from galaxy.tools.parameters.basic import (
@@ -187,6 +189,26 @@ def process_key(incoming_key: str, incoming_value: Any, d: Dict[str, Any]):
         process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)
 
 
+def nested_key_to_path(key: str) -> Sequence[Union[str, int]]:
+    """
+    Convert a tool state key that is separated with '|' and '_n' into path iterable.
+    E.g. "cond|repeat_0|paramA" -> ["cond", "repeat", 0, "paramA"].
+    Return value can be used with `boltons.iterutils.get_path`.
+    """
+    path: List[Union[str, int]] = []
+    key_parts = key.split("|")
+    if len(key_parts) == 1:
+        return key_parts
+    for key_part in key_parts:
+        if "_" in key_part:
+            input_name, _index = key_part.rsplit("_", 1)
+            if _index.isdigit():
+                path.extend((input_name, int(_index)))
+                continue
+        path.append(key_part)
+    return path
+
+
 def flat_to_nested_state(incoming: Dict[str, Any]):
     nested_state: Dict[str, Any] = {}
     for key, value in incoming.items():
@@ -194,4 +216,11 @@ def flat_to_nested_state(incoming: Dict[str, Any]):
     return nested_state
 
 
-__all__ = ("LegacyUnprefixedDict", "WrappedParameters", "make_dict_copy", "process_key", "flat_to_nested_state")
+__all__ = (
+    "LegacyUnprefixedDict",
+    "WrappedParameters",
+    "make_dict_copy",
+    "process_key",
+    "flat_to_nested_state",
+    "nested_key_to_path",
+)

lib/galaxy/workflow/run.py

@@ -10,6 +10,7 @@ from typing import (
     Union,
 )
 
+from boltons.iterutils import get_path
 from typing_extensions import Protocol
 
 from galaxy import model
@@ -35,6 +36,7 @@ from galaxy.schema.invocation import (
     WarningReason,
 )
 from galaxy.tools.parameters.basic import raw_to_galaxy
+from galaxy.tools.parameters.wrapped import nested_key_to_path
 from galaxy.util import ExecutionTimer
 from galaxy.workflow import modules
 from galaxy.workflow.run_request import (
@@ -444,6 +446,10 @@ class WorkflowProgress:
                     replacement = temp
             else:
                 replacement = self.replacement_for_connection(connection[0], is_data=is_data)
+        elif step.state and (state_input := get_path(step.state.inputs, nested_key_to_path(prefixed_name), None)):
+            # workflow submitted with step parameters populates state directly
+            # via populate_module_and_state
+            replacement = state_input
         else:
             for step_input in step.inputs:
                 if step_input.name == prefixed_name and step_input.default_value_set:

lib/galaxy_test/api/test_workflows.py

@@ -6982,6 +6982,35 @@ steps:
             # Take a valid stat and make it invalid, assert workflow won't run.
             self._assert_status_code_is(invocation_response, 400)
 
+    @skip_without_tool("collection_paired_test")
+    def test_run_map_over_with_step_parameter_dict(self):
+        # Tests what the legacy run form submits
+        with self.dataset_populator.test_history() as history_id:
+            hdca = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()["outputs"][0]
+            workflow_id = self._upload_yaml_workflow(
+                """
+class: GalaxyWorkflow
+steps:
+  "0":
+    tool_id: collection_paired_conditional_structured_like
+    state:
+      cond:
+        input1:
+          __class__: RuntimeValue
+"""
+            )
+            workflow_request = {
+                "history": f"hist_id={history_id}",
+                "parameters": dumps({"0": {"cond|input1": {"values": [{"id": hdca["id"], "src": "hdca"}]}}}),
+                "parameters_normalized": True,
+            }
+            url = f"workflows/{workflow_id}/invocations"
+            invocation_response = self._post(url, data=workflow_request, json=True)
+            invocation_response.raise_for_status()
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id=history_id, workflow_id=workflow_id, invocation_id=invocation_response.json()["id"]
+            )
+
     @skip_without_tool("validation_default")
     def test_parameter_substitution_validation_value_errors_1(self):
         substitions = dict(select_param='" ; echo "moo')

test/unit/app/tools/test_parameter_parsing.py

@@ -3,10 +3,28 @@ from typing import (
     Dict,
 )
 
-from galaxy.tools.parameters.wrapped import process_key
+from galaxy.tools.parameters.wrapped import (
+    nested_key_to_path,
+    process_key,
+)
 from .util import BaseParameterTestCase
 
 
+def test_nested_key_to_path():
+    assert nested_key_to_path("param") == ["param"]
+    assert nested_key_to_path("param_x") == ["param_x"]
+    assert nested_key_to_path("cond|param_x") == ["cond", "param_x"]
+    assert nested_key_to_path("param_") == ["param_"]
+    assert nested_key_to_path("cond|param_") == ["cond", "param_"]
+    assert nested_key_to_path("repeat_1|inner_repeat_1|data_table_column_value") == [
+        "repeat",
+        1,
+        "inner_repeat",
+        1,
+        "data_table_column_value",
+    ]
+
+
 class TestProcessKey:
     def test_process_key(self):
         nested_dict: Dict[str, Any] = {}