Merge branch 'release_24.2' into dev

client/src/components/Panels/Common/ToolSearch.vue

@@ -80,7 +80,9 @@ const localFilterText = computed({
         return props.query !== null ? props.query : "";
     },
     set: (newVal: any) => {
-        checkQuery(newVal);
+        if (newVal.trim() || props.query.trim()) {
+            checkQuery(newVal);
+        }
     },
 });
 

client/src/viz/trackster.js

@@ -74,23 +74,30 @@ export class TracksterUI extends Backbone.Model {
             },
             bookmarks: bookmarks,
         };
-
-        // Make call to save visualization.
-        return $.ajax({
-            url: `${getAppRoot()}visualization/save`,
-            type: "POST",
+        const request = {
             dataType: "json",
-            data: {
+            contentType: "application/json; charset=utf-8",
+            data: JSON.stringify({
                 id: this.view.vis_id,
                 title: this.view.config.get_value("name"),
                 dbkey: this.view.dbkey,
                 type: "trackster",
-                vis_json: JSON.stringify(viz_config),
-            },
-        })
+                config: viz_config,
+            }),
+        };
+        if (!this.view.vis_id) {
+            request.url = `${getAppRoot()}api/visualizations`;
+            request.type = "POST";
+        } else {
+            request.url = `${getAppRoot()}api/visualizations/${this.view.vis_id}`;
+            request.type = "PUT";
+        }
+
+        // Make call to save visualization.
+        return $.ajax(request)
             .success((vis_info) => {
                 Galaxy.modal.hide();
-                this.view.vis_id = vis_info.vis_id;
+                this.view.vis_id = vis_info.id;
                 this.view.has_changes = false;
 
                 // Needed to set URL when first saving a visualization.

lib/galaxy/managers/jobs.py

@@ -345,7 +345,7 @@ def get_job_console_output(
 
     def stop(self, job, message=None):
         if not job.finished:
-            job.mark_deleted(self.app.config.track_jobs_in_database)
+            job.mark_deleted(self.app.config.track_jobs_in_database, message)
             session = self.app.model.session
             session.commit()
             self.app.job_manager.stop(job, message=message)
@@ -391,7 +391,12 @@ def populate_input_data_input_id(path, key, value):
                 current_case = param_dump
                 for p in path:
                     current_case = current_case[p]
-                src = current_case["src"]
+                src = current_case.get("src")
+                if src is None:
+                    # just a parameter named id.
+                    # TODO: dispatch on tool parameter type instead of values,
+                    # maybe with tool state variant
+                    return key, value
                 current_case = param
                 for i, p in enumerate(path):
                     if p == "values" and i == len(path) - 2:

lib/galaxy/model/__init__.py

@@ -1893,7 +1893,7 @@ def mark_stopped(self, track_jobs_in_database=False):
         else:
             self.state = Job.states.STOPPED
 
-    def mark_deleted(self, track_jobs_in_database=False):
+    def mark_deleted(self, track_jobs_in_database=False, message=None):
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
@@ -1904,7 +1904,8 @@ def mark_deleted(self, track_jobs_in_database=False):
             self.state = Job.states.DELETING
         else:
             self.state = Job.states.DELETED
-        self.info = "Job output deleted by user before job completed."
+        info = message or "Job output deleted by user before job completed."
+        self.info = info
         for jtoda in self.output_datasets:
             output_hda = jtoda.dataset
             output_hda.deleted = True
@@ -1914,7 +1915,7 @@ def mark_deleted(self, track_jobs_in_database=False):
                 shared_hda.deleted = True
                 shared_hda.blurb = "deleted"
                 shared_hda.peek = "Job deleted"
-                shared_hda.info = "Job output deleted by user before job completed"
+                shared_hda.info = info
 
     def mark_failed(self, info="Job execution failed", blurb=None, peek=None):
         """
@@ -3686,6 +3687,10 @@ def active_contents(self):
         """Return all active contents ordered by hid."""
         return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)
 
+    @property
+    def visible_contents(self):
+        return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)
+
     def contents_iter(self, **kwds):
         """
         Fetch filtered list of contents of history.
@@ -4979,11 +4984,16 @@ def display_name(self):
     def display_info(self):
         return self.datatype.display_info(self)
 
-    def get_converted_files_by_type(self, file_type):
+    def get_converted_files_by_type(self, file_type, include_errored=False):
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and assoc.type == file_type:
                 item = assoc.dataset or assoc.dataset_ldda
-                if not item.deleted and item.state in Dataset.valid_input_states:
+                valid_states = (
+                    (Dataset.states.ERROR, *Dataset.valid_input_states)
+                    if include_errored
+                    else Dataset.valid_input_states
+                )
+                if not item.deleted and item.state in valid_states:
                     return item
         return None
 
@@ -4998,7 +5008,7 @@ def get_converted_dataset_deps(self, trans, target_ext):
             depends_list = []
         return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}
 
-    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
+    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):
         """
         Return converted dataset(s) if they exist, along with a dict of dependencies.
         If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -5010,7 +5020,7 @@ def get_converted_dataset(self, trans, target_ext, target_context=None, history=
         converted_dataset = self.get_metadata_dataset(target_ext)
         if converted_dataset:
             return converted_dataset
-        converted_dataset = self.get_converted_files_by_type(target_ext)
+        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)
         if converted_dataset:
             return converted_dataset
         deps = {}
@@ -5232,7 +5242,8 @@ def convert_dataset(self, trans, target_type):
 
         # Get converted dataset; this will start the conversion if necessary.
         try:
-            converted_dataset = self.get_converted_dataset(trans, target_type)
+            # Include errored datasets here, we let user chose to retry or view error
+            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)
         except NoConverterException:
             return self.conversion_messages.NO_CONVERTER
         except ConverterDependencyException as dep_error:
@@ -7871,7 +7882,7 @@ class Workflow(Base, Dictifiable, RepresentById):
     source_metadata: Mapped[Optional[Dict[str, str]]] = mapped_column(JSONType)
     uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)
 
-    steps = relationship(
+    steps: Mapped[List["WorkflowStep"]] = relationship(
         "WorkflowStep",
         back_populates="workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
@@ -7921,7 +7932,7 @@ def to_dict(self, view="collection", value_mapper=None):
         return rval
 
     @property
-    def steps_by_id(self):
+    def steps_by_id(self) -> Dict[int, "WorkflowStep"]:
         steps = {}
         for step in self.steps:
             step_id = step.id
@@ -8096,7 +8107,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         back_populates="workflow_step",
     )
     post_job_actions = relationship("PostJobAction", back_populates="workflow_step")
-    inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
+    inputs: Mapped[List["WorkflowStepInput"]] = relationship("WorkflowStepInput", back_populates="workflow_step")
     workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship(back_populates="workflow_step")
     output_connections: Mapped[List["WorkflowStepConnection"]] = relationship(
         primaryjoin=(lambda: WorkflowStepConnection.output_step_id == WorkflowStep.id)
@@ -8436,16 +8447,16 @@ class WorkflowStepConnection(Base, RepresentById):
     output_name: Mapped[Optional[str]] = mapped_column(TEXT)
     input_subworkflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
 
-    input_step_input = relationship(
+    input_step_input: Mapped["WorkflowStepInput"] = relationship(
         "WorkflowStepInput",
         back_populates="connections",
         cascade="all",
         primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
     )
-    input_subworkflow_step = relationship(
+    input_subworkflow_step: Mapped[Optional["WorkflowStep"]] = relationship(
         "WorkflowStep", primaryjoin=(lambda: WorkflowStepConnection.input_subworkflow_step_id == WorkflowStep.id)
     )
-    output_step = relationship(
+    output_step: Mapped["WorkflowStep"] = relationship(
         "WorkflowStep",
         back_populates="output_connections",
         cascade="all",
@@ -8469,7 +8480,7 @@ def input_name(self):
 
     @property
     def input_step(self) -> Optional[WorkflowStep]:
-        return self.input_step_input and self.input_step_input.workflow_step
+        return self.input_step_input.workflow_step
 
     @property
     def input_step_id(self):
@@ -8678,7 +8689,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         back_populates="workflow_invocation",
         order_by=lambda: WorkflowInvocationStep.order_index,
     )
-    workflow = relationship("Workflow")
+    workflow: Mapped[Workflow] = relationship("Workflow")
     output_dataset_collections = relationship(
         "WorkflowInvocationOutputDatasetCollectionAssociation",
         back_populates="workflow_invocation",
@@ -9594,7 +9605,7 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable):
         ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"))
-    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    value: Mapped[Optional[Dict[str, Any]]] = mapped_column(MutableJSONType)
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()
     workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="step_states")
 

lib/galaxy/tool_util/toolbox/__init__.py

@@ -3,6 +3,7 @@
 from .base import (
     AbstractToolBox,
     AbstractToolTagManager,
+    ToolLoadConfigurationConflict,
     ToolLoadError,
 )
 from .panel import (
@@ -15,6 +16,7 @@
     "AbstractToolBox",
     "AbstractToolTagManager",
     "panel_item_types",
+    "ToolLoadConfigurationConflict",
     "ToolLoadError",
     "ToolSection",
     "ToolSectionLabel",

lib/galaxy/tool_util/toolbox/base.py

@@ -141,6 +141,10 @@ class ToolLoadError(Exception):
     pass
 
 
+class ToolLoadConfigurationConflict(Exception):
+    pass
+
+
 class AbstractToolBox(ManagesIntegratedToolPanelMixin):
     """
     Abstract container for managing a ToolPanel - containing tools and
@@ -1081,6 +1085,8 @@ def quick_load(tool_file, async_load=True):
                     self._load_tool_panel_views()
                     self._save_integrated_tool_panel()
                 return tool.id
+            except ToolLoadConfigurationConflict as e:
+                log.warning(f"Configuration does not permit loading tool {tool_file} - {e}")
             except ToolLoadError as e:
                 # no need for full stack trace - ToolLoadError corresponds to a known load
                 # error with defined cause that is included in the message

lib/galaxy/tools/__init__.py

@@ -98,6 +98,7 @@
 from galaxy.tool_util.toolbox import (
     AbstractToolBox,
     AbstractToolTagManager,
+    ToolLoadConfigurationConflict,
     ToolLoadError,
     ToolSection,
 )
@@ -3194,7 +3195,9 @@ class InteractiveTool(Tool):
 
     def __init__(self, config_file, tool_source, app, **kwd):
         if not app.config.interactivetools_enable:
-            raise ToolLoadError("Trying to load an InteractiveTool, but InteractiveTools are not enabled.")
+            raise ToolLoadConfigurationConflict(
+                "Trying to load an InteractiveTool, but InteractiveTools are not enabled."
+            )
         super().__init__(config_file, tool_source, app, **kwd)
 
     def __remove_interactivetool_by_job(self, job):

lib/galaxy/web/framework/base.py

@@ -492,7 +492,7 @@ def __init__(self):
         """
         Create a new Response defaulting to HTML content and "200 OK" status
         """
-        self.status = "200 OK"
+        self.status: int = 200
         self.headers = HeaderDict({"content-type": "text/html; charset=UTF-8"})
         self.cookies = SimpleCookie()