Merge branch 'release_23.2' into dev

client/src/api/schema/schema.ts

@@ -6809,7 +6809,7 @@ export interface components {
              * Value
              * @description The values of the job parameter
              */
-            value: Record<string, never>;
+            value?: Record<string, never>;
         };
         /**
          * JobSourceType

client/src/components/History/Index.vue

@@ -1,5 +1,8 @@
 <template>
-    <div v-if="currentUser && currentHistory" id="current-history-panel" class="d-flex flex-column history-index">
+    <div
+        v-if="currentUser && currentHistory"
+        id="current-history-panel"
+        class="d-flex flex-column history-index overflow-auto">
         <HistoryPanel
             v-if="!breadcrumbs.length"
             :list-offset="listOffset"

client/src/components/Panels/Menus/PanelViewMenu.vue

@@ -1,5 +1,14 @@
 <template>
+    <b-button
+        v-if="showAdvanced"
+        variant="link"
+        class="w-100"
+        size="sm"
+        @click="$emit('update:show-advanced', !showAdvanced)">
+        <slot name="panel-view-selector"></slot><span class="sr-only">Close advanced tool search menu</span>
+    </b-button>
     <b-dropdown
+        v-else
         v-b-tooltip.hover.top.noninteractive
         right
         block
@@ -59,6 +68,10 @@ export default {
         currentPanelView: {
             type: String,
         },
+        showAdvanced: {
+            type: Boolean,
+            default: false,
+        },
         storeLoading: {
             type: Boolean,
             default: false,

client/src/components/Panels/ToolPanel.vue

@@ -139,6 +139,7 @@ function onInsertWorkflowSteps(workflowId: string, workflowStepCount: number | u
                     v-if="panelViews && Object.keys(panelViews).length > 1"
                     :panel-views="panelViews"
                     :current-panel-view="currentPanelView"
+                    :show-advanced.sync="showAdvanced"
                     :store-loading="loading"
                     @updatePanelView="updatePanelView">
                     <template v-slot:panel-view-selector>

client/src/components/SingleItemSelector.vue

@@ -4,7 +4,7 @@
         <Multiselect
             v-if="items"
             v-model="selectedItem"
-            deselect-label="Can't remove this value"
+            :deselect-label="null"
             track-by="id"
             label="text"
             :options="items"

lib/galaxy/datatypes/display_applications/parameters.py

@@ -1,11 +1,12 @@
 # Contains parameters that are used in Display Applications
 import mimetypes
+from dataclasses import dataclass
 from typing import Optional
 from urllib.parse import quote_plus
 
 from galaxy.model.base import transaction
+from galaxy.schema.schema import DatasetState
 from galaxy.util import string_as_bool
-from galaxy.util.bunch import Bunch
 from galaxy.util.template import fill_template
 
 DEFAULT_DATASET_NAME = "dataset"
@@ -57,6 +58,13 @@ def build_url(self, other_values):
         return fill_template(self.url, context=other_values)
 
 
+@dataclass
+class DatasetLikeObject:
+    file_name: str
+    state: DatasetState
+    extension: str
+
+
 class DisplayApplicationDataParameter(DisplayApplicationParameter):
     """Parameter that returns a file_name containing the requested content"""
 
@@ -95,27 +103,29 @@ def formats(self):
             )
         return None
 
-    def _get_dataset_like_object(self, other_values):
+    def _get_dataset_like_object(self, other_values) -> Optional[DatasetLikeObject]:
         # this returned object has file_name, state, and states attributes equivalent to a DatasetAssociation
         data = other_values.get(self.dataset, None)
         assert data, "Base dataset could not be found in values provided to DisplayApplicationDataParameter"
         if isinstance(data, DisplayDataValueWrapper):
             data = data.value
-        if data.state != data.states.OK:
+        if data.state != DatasetState.OK:
             return None
         if self.metadata:
             rval = getattr(data.metadata, self.metadata, None)
             assert rval, f'Unknown metadata name "{self.metadata}" provided for dataset type "{data.ext}".'
-            return Bunch(file_name=rval.get_file_name(), state=data.state, states=data.states, extension="data")
-        elif self.extensions and (self.force_conversion or not isinstance(data.datatype, self.formats)):
+            return DatasetLikeObject(file_name=rval.get_file_name(), state=data.state, extension="data")
+        elif (
+            self.formats and self.extensions and (self.force_conversion or not isinstance(data.datatype, self.formats))
+        ):
             for ext in self.extensions:
                 rval = data.get_converted_files_by_type(ext)
                 if rval:
-                    return rval
+                    return DatasetLikeObject(file_name=rval.get_file_name(), state=rval.state, extension=rval.extension)
             direct_match, target_ext, _ = data.find_conversion_destination(self.formats)
             assert direct_match or target_ext is not None, f"No conversion path found for data param: {self.name}"
             return None
-        return data
+        return DatasetLikeObject(file_name=data.get_file_name(), state=data.state, extension=data.extension)
 
     def get_value(self, other_values, dataset_hash, user_hash, trans):
         if data := self._get_dataset_like_object(other_values):
@@ -153,21 +163,21 @@ def prepare(self, other_values, dataset_hash, user_hash, trans):
                     trans.sa_session.add(assoc)
                     with transaction(trans.sa_session):
                         trans.sa_session.commit()
-                elif converted_dataset and converted_dataset.state == converted_dataset.states.ERROR:
+                elif converted_dataset and converted_dataset.state == DatasetState.ERROR:
                     raise Exception(f"Dataset conversion failed for data parameter: {self.name}")
         return self.get_value(other_values, dataset_hash, user_hash, trans)
 
     def is_preparing(self, other_values):
         value = self._get_dataset_like_object(other_values)
-        if value and value.state in (value.states.NEW, value.states.UPLOAD, value.states.QUEUED, value.states.RUNNING):
+        if value and value.state in (DatasetState.NEW, DatasetState.UPLOAD, DatasetState.QUEUED, DatasetState.RUNNING):
             return True
         return False
 
     def ready(self, other_values):
         if value := self._get_dataset_like_object(other_values):
-            if value.state == value.states.OK:
+            if value.state == DatasetState.OK:
                 return True
-            elif value.state == value.states.ERROR:
+            elif value.state == DatasetState.ERROR:
                 raise Exception(f"A data display parameter is in the error state: {self.name}")
         return False
 

lib/galaxy/schema/jobs.py

@@ -225,7 +225,7 @@ class JobParameter(Model):
         title="Depth",
         description="The depth of the job parameter.",
     )
-    value: Any = Field(default=Required, title="Value", description="The values of the job parameter")
+    value: Optional[Any] = Field(default=None, title="Value", description="The values of the job parameter")
     notes: Optional[str] = Field(default=None, title="Notes", description="Notes associated with the job parameter.")
 
 

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -673,7 +673,7 @@ def display_application(
                                     ), f"Extra file content requested ({action_param_extra}), but allow_extra_files_access is False."
                                     file_name = os.path.join(value.extra_files_path, action_param_extra)
                                 else:
-                                    file_name = value.get_file_name()
+                                    file_name = value.file_name
                                 content_length = os.path.getsize(file_name)
                                 rval = open(file_name, "rb")
                             except OSError as e: