Merge branch 'release_24.2' into dev

client/src/components/ActivityBar/ActivitySettings.vue

@@ -70,8 +70,8 @@ function executeActivity(activity: Activity) {
 </script>
 
 <template>
-    <div class="activity-settings rounded no-highlight">
-        <div v-if="foundActivities" class="activity-settings-content">
+    <div>
+        <div v-if="foundActivities">
             <button
                 v-for="activity in filteredActivities"
                 :key="activity.id"
@@ -122,7 +122,7 @@ function executeActivity(activity: Activity) {
                 </div>
             </button>
         </div>
-        <div v-else class="activity-settings-content">
+        <div v-else>
             <b-alert v-localize class="py-1 px-2" show> No matching activities found. </b-alert>
         </div>
     </div>
@@ -131,23 +131,14 @@ function executeActivity(activity: Activity) {
 <style lang="scss">
 @import "theme/blue.scss";
 
-.activity-settings {
-    overflow-y: hidden;
-    display: flex;
-    flex-direction: column;
-}
-
-.activity-settings-content {
-    overflow-y: auto;
-}
-
 .activity-settings-item {
     background: none;
     border: none;
     text-align: left;
     transition: none;
     width: 100%;
 }
+
 .activity-settings-item:hover {
     background: $gray-200;
 }

client/src/components/Panels/VisualizationPanel.vue

@@ -104,11 +104,11 @@ onMounted(() => {
             <h3>Create Visualization</h3>
             <DelayedInput :delay="100" placeholder="Search visualizations" @change="query = $event" />
         </template>
-        <div class="overflow-y mt-2">
+        <div>
             <LoadingSpan v-if="isLoading" message="Loading visualizations" />
             <div v-else-if="filteredPlugins.length > 0">
                 <div v-for="plugin in filteredPlugins" :key="plugin.name">
-                    <button :data-plugin-name="plugin.name" @click="selectVisualization(plugin)">
+                    <button class="plugin-item" :data-plugin-name="plugin.name" @click="selectVisualization(plugin)">
                         <div class="d-flex">
                             <div class="plugin-thumbnail mr-2">
                                 <img v-if="plugin.logo" alt="visualization" :src="absPath(plugin.logo)" />
@@ -143,6 +143,20 @@ onMounted(() => {
 </template>
 
 <style lang="scss">
+@import "theme/blue.scss";
+
+.plugin-item {
+    background: none;
+    border: none;
+    text-align: left;
+    transition: none;
+    width: 100%;
+}
+
+.plugin-item:hover {
+    background: $gray-200;
+}
+
 .plugin-thumbnail {
     img {
         width: 2rem;

lib/galaxy/model/__init__.py

@@ -8103,7 +8103,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
     tool_errors: Mapped[Optional[bytes]] = mapped_column(JSONType)
     position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     config: Mapped[Optional[bytes]] = mapped_column(JSONType)
-    order_index: Mapped[Optional[int]]
+    order_index: Mapped[int]
     when_expression: Mapped[Optional[bytes]] = mapped_column(JSONType)
     uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)
     label: Mapped[Optional[str]] = mapped_column(Unicode(255))
@@ -8201,17 +8201,18 @@ def setup_inputs_by_name(self):
         # Ensure input_connections has already been set.
 
         # Make connection information available on each step by input name.
-        inputs_by_name = {}
+        inputs_by_name: Dict[str, Any] = {}
         for step_input in self.inputs:
             input_name = step_input.name
             assert input_name not in inputs_by_name
             inputs_by_name[input_name] = step_input
         self._inputs_by_name = inputs_by_name
+        return inputs_by_name
 
     @property
     def inputs_by_name(self):
         if self._inputs_by_name is None:
-            self.setup_inputs_by_name()
+            return self.setup_inputs_by_name()
         return self._inputs_by_name
 
     def get_input(self, input_name):
@@ -8690,7 +8691,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
     scheduler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
-    uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType())
+    uuid: Mapped[Optional[Union[UUID]]] = mapped_column(UUIDType())
     history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)
 
     history = relationship("History", back_populates="workflow_invocations")
@@ -9415,7 +9416,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
     )
     action: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
 
-    workflow_step = relationship("WorkflowStep")
+    workflow_step: Mapped[WorkflowStep] = relationship("WorkflowStep")
     job: Mapped[Optional["Job"]] = relationship(back_populates="workflow_invocation_step", uselist=False)
     implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False)
     output_dataset_collections = relationship(

lib/galaxy/model/store/ro_crate_utils.py

@@ -358,6 +358,7 @@ def _add_step_parameter_pv(self, step: WorkflowInvocationStep, crate: ROCrate):
 
     def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
         param_id = step.workflow_step.label
+        assert step.workflow_step.tool_inputs
         param_type = step.workflow_step.tool_inputs["parameter_type"]
         return crate.add(
             ContextEntity(
@@ -375,6 +376,7 @@ def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
 
     def _add_step_tool_pv(self, step: WorkflowInvocationStep, tool_input: str, crate: ROCrate):
         param_id = tool_input
+        assert step.workflow_step.tool_inputs
         return crate.add(
             ContextEntity(
                 crate,

lib/galaxy/tool_util/deps/conda_util.py

@@ -48,7 +48,7 @@
 VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
 UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
 USE_PATH_EXEC_DEFAULT = False
-CONDA_PACKAGE_SPECS = ("conda>=23.7.0", "conda-libmamba-solver", "'pyopenssl>=22.1.0'")
+CONDA_PACKAGE_SPECS = ("conda>=23.7.0", "conda-libmamba-solver", "pyopenssl>=22.1.0")
 CONDA_BUILD_SPECS = ("conda-build>=3.22.0",)
 USE_LOCAL_DEFAULT = False
 

lib/galaxy/tools/parameters/__init__.py

@@ -31,6 +31,7 @@
 )
 from .workflow_utils import (
     is_runtime_value,
+    NO_REPLACEMENT,
     runtime_to_json,
 )
 from .wrapped import flat_to_nested_state
@@ -174,14 +175,36 @@ def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefi
         if input.name not in input_values:
             args["error"] = f"No value found for '{args.get('prefixed_label')}'."
         new_value = callback(**args)
+
+        # is this good enough ? feels very ugh
+        if new_value == [no_replacement_value]:
+            # Single unspecified value in multiple="true" input with a single null input, pretend it's a singular value
+            new_value = no_replacement_value
+        if isinstance(new_value, list):
+            # Maybe mixed input, I guess tool defaults don't really make sense here ?
+            # Would e.g. be default dataset in multiple="true" input, you wouldn't expect the default to be inserted
+            # if other inputs are connected and provided.
+            new_value = [item if not item == no_replacement_value else None for item in new_value]
+
         if no_replacement_value is REPLACE_ON_TRUTHY:
             replace = bool(new_value)
         else:
             replace = new_value != no_replacement_value
         if replace:
             input_values[input.name] = new_value
-        elif replace_optional_connections and is_runtime_value(value) and hasattr(input, "value"):
-            input_values[input.name] = input.value
+        elif replace_optional_connections:
+            # Only used in workflow context
+            has_default = hasattr(input, "value")
+            if new_value is value is NO_REPLACEMENT or is_runtime_value(value):
+                # NO_REPLACEMENT means value was connected but left unspecified
+                if has_default:
+                    # Use default if we have one
+                    input_values[input.name] = input.value
+                else:
+                    # Should fail if input is not optional and does not have default value
+                    # Effectively however depends on parameter implementation.
+                    # We might want to raise an exception here, instead of depending on a tool parameter value error.
+                    input_values[input.name] = None
 
     def get_current_case(input, input_values):
         test_parameter = input.test_param

lib/galaxy/tools/parameters/basic.py

@@ -49,7 +49,10 @@
     ParameterParseException,
     text_input_is_optional,
 )
-from galaxy.tools.parameters.workflow_utils import workflow_building_modes
+from galaxy.tools.parameters.workflow_utils import (
+    NO_REPLACEMENT,
+    workflow_building_modes,
+)
 from galaxy.util import (
     sanitize_param,
     string_as_bool,
@@ -247,6 +250,8 @@ def to_python(self, value, app):
     def value_to_basic(self, value, app, use_security=False):
         if is_runtime_value(value):
             return runtime_to_json(value)
+        elif value == NO_REPLACEMENT:
+            return {"__class__": "NoReplacement"}
         return self.to_json(value, app, use_security)
 
     def value_from_basic(self, value, app, ignore_errors=False):
@@ -255,8 +260,11 @@ def value_from_basic(self, value, app, ignore_errors=False):
             if isinstance(self, HiddenToolParameter):
                 raise ParameterValueError(message_suffix="Runtime Parameter not valid", parameter_name=self.name)
             return runtime_to_object(value)
-        elif isinstance(value, MutableMapping) and value.get("__class__") == "UnvalidatedValue":
-            return value["value"]
+        elif isinstance(value, MutableMapping):
+            if value.get("__class__") == "UnvalidatedValue":
+                return value["value"]
+            elif value.get("__class__") == "NoReplacement":
+                return NO_REPLACEMENT
         # Delegate to the 'to_python' method
         try:
             return self.to_python(value, app)

lib/galaxy/tools/parameters/workflow_utils.py

@@ -1,6 +1,15 @@
 from collections.abc import MutableMapping
 
 
+class NoReplacement:
+
+    def __str__(self):
+        return "NO_REPLACEMENT singleton"
+
+
+NO_REPLACEMENT = NoReplacement()
+
+
 class workflow_building_modes:
     DISABLED = False
     ENABLED = True