Merge pull request #16768 from mvdbeek/dev

Merge release_23.1 into dev

client/src/components/Form/Elements/FormSelect.vue

@@ -127,7 +127,7 @@ onMounted(() => {
         v-if="hasOptions"
         :id="id"
         v-model="currentValue"
-        :allow-empty="multiple && optional"
+        :allow-empty="optional"
         :aria-expanded="ariaExpanded"
         :close-on-select="!multiple"
         :disabled="disabled"

client/src/components/Workflow/Editor/NodeOutput.vue

@@ -110,9 +110,9 @@ const visibleHint = computed(() => {
     }
 });
 const label = computed(() => {
-    const activeLabel = workflowOutput.value?.label || props.output.name;
-    return `${activeLabel} (${extensions.value.join(", ")})`;
+    return workflowOutput.value?.label || props.output.name;
 });
+
 const rowClass = computed(() => {
     const classes = ["form-row", "dataRow", "output-data-row"];
     if ("valid" in props.output && props.output?.valid === false) {
@@ -153,7 +153,7 @@ function onToggleActive() {
             (workflowOutput) => workflowOutput.output_name !== output.value.name
         );
     } else {
-        stepWorkflowOutputs.push({ output_name: output.value.name });
+        stepWorkflowOutputs.push({ output_name: output.value.name, label: output.value.name });
     }
     stepStore.updateStep({ ...step, workflow_outputs: stepWorkflowOutputs });
 }
@@ -290,6 +290,22 @@ const outputDetails = computed(() => {
     return outputType;
 });
 
+const isDuplicateLabel = computed(() => {
+    const duplicateLabels = stepStore.duplicateLabels;
+    return Boolean(label.value && duplicateLabels.has(label.value));
+});
+
+const labelClass = computed(() => {
+    if (isDuplicateLabel.value) {
+        return "alert-info";
+    }
+    return null;
+});
+
+const labelToolTipTitle = computed(() => {
+    return `Output label '${workflowOutput.value?.label}' is not unique`;
+});
+
 onBeforeUnmount(() => {
     stateStore.deleteOutputTerminalPosition(props.stepId, props.output.name);
 });
@@ -327,8 +343,16 @@ const removeTagsAction = computed(() => {
                     <FontAwesomeIcon v-if="isVisible" fixed-width icon="fa-eye" />
                     <FontAwesomeIcon v-else fixed-width icon="fa-eye-slash" />
                 </button>
-                <span class="ml-1">
-                    {{ label }}
+                <span>
+                    <span
+                        v-b-tooltip
+                        :title="labelToolTipTitle"
+                        class="d-inline-block rounded"
+                        :class="labelClass"
+                        :disabled="!isDuplicateLabel">
+                        {{ label }}
+                    </span>
+                    <span> ({{ extensions.join(", ") }}) </span>
                 </span>
             </div>
 

client/src/stores/workflowStepStore.ts

@@ -183,6 +183,23 @@ export const useWorkflowStepStore = (workflowId: string) => {
                 });
                 return workflowOutputs;
             },
+            duplicateLabels(state: State) {
+                const duplicateLabels: Set<string> = new Set();
+                const labels: Set<string> = new Set();
+                Object.values(state.steps).forEach((step) => {
+                    if (step.workflow_outputs?.length) {
+                        step.workflow_outputs.forEach((workflowOutput) => {
+                            if (workflowOutput.label) {
+                                if (labels.has(workflowOutput.label)) {
+                                    duplicateLabels.add(workflowOutput.label);
+                                }
+                                labels.add(workflowOutput.label);
+                            }
+                        });
+                    }
+                });
+                return duplicateLabels;
+            },
         },
         actions: {
             addStep(newStep: NewStep): Step {

client/src/utils/navigation/navigation.yml

@@ -670,7 +670,7 @@ workflow_editor:
       clone: '${_} .node-clone'
       output_data_row:
         type: xpath
-        selector: '//div[contains(@class, "output-data-row") and contains(string(), "${output_name} (${extension})")]'
+        selector: '//div[@data-output-name="${output_name}"]//span[contains(text(), "(${extension})")]'
       output_terminal: "${_} [output-name='${name}']"
       input_terminal: "${_} [input-name='${name}']"
       input_mapping_icon: "${_} [input-name='${name}'].mapped-over"

doc/source/releases/23.1_announce.rst

@@ -200,6 +200,8 @@ Deprecation Notices
 
 The first Galaxy release of 2024 (24.0) will drop support for Python 3.7, which has already reached end of life (EOL).
 
+The **api/search** API endpoint is deprecated and will be removed in the next release.
+
 Release Notes
 ===========================================================
 

lib/galaxy/model/__init__.py

@@ -8363,7 +8363,7 @@ def to_dict(self, view="collection", value_mapper=None, step_details=False, lega
                 # TODO: does this work correctly if outputs are mapped over?
                 label = output_assoc.workflow_output.label
                 if not label:
-                    continue
+                    label = f"{output_assoc.workflow_output.output_name} (Step {output_assoc.workflow_output.workflow_step.order_index + 1})"
 
                 outputs[label] = {
                     "src": "hda",
@@ -8375,7 +8375,9 @@ def to_dict(self, view="collection", value_mapper=None, step_details=False, lega
             for output_assoc in self.output_dataset_collections:
                 label = output_assoc.workflow_output.label
                 if not label:
-                    continue
+                    label = (
+                        label
+                    ) = f"{output_assoc.workflow_output.output_name} (Step {output_assoc.workflow_output.workflow_step.order_index + 1})"
 
                 output_collections[label] = {
                     "src": "hdca",

tools/filters/CreateInterval.xml

@@ -1,5 +1,8 @@
 <tool id="createInterval" name="Create single interval" version="1.0.0">
   <description>as a new dataset</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <command>
 perl '$__tool_directory__/CreateInterval.pl' '$chrom' $start $end '$name' $strand '$out_file1'
   </command>

tools/filters/changeCase.xml

@@ -1,5 +1,8 @@
 <tool id="ChangeCase" name="Change Case" version="1.0.0">
   <description> of selected columns</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <stdio>
     <exit_code range="1:" err_level="fatal" />
   </stdio>

tools/filters/commWrapper.xml

@@ -1,5 +1,8 @@
 <tool id="Comm1" name="Find Similarities and Differences" version="1.0.0">
   <description>between two datasets</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>

tools/filters/condense_characters.xml

@@ -1,5 +1,8 @@
 <tool id="Condense characters1" name="Condense" version="1.0.0">
   <description>consecutive characters</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <command><![CDATA[
 perl '$__tool_directory__/condense_characters.pl'
 '$input'

tools/filters/cutWrapper.xml

@@ -1,5 +1,8 @@
 <tool id="Cut1" name="Cut" version="1.0.2">
   <description>columns from a table</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>

tools/filters/pasteWrapper.xml

@@ -1,5 +1,9 @@
 <tool id="Paste1" name="Paste" version="1.0.0">
   <description>two files side by side</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+    <requirement type="package" version="8.31">coreutils</requirement>
+  </requirements>
   <command>perl '$__tool_directory__/pasteWrapper.pl' '$input1' '$input2' $delimiter '$out_file1'</command>
   <inputs>
 <!--    <display>paste $input1 and $input2 using $delimiter as delimiter</display> -->

tools/filters/remove_beginning.xml

@@ -1,5 +1,8 @@
 <tool id="Remove beginning1" name="Remove beginning" version="1.0.0">
   <description>of a file</description>
+  <requirements>
+    <requirement type="package" version="5.26">perl</requirement>
+  </requirements>
   <command>
 perl '$__tool_directory__/remove_beginning.pl' '$input' $num_lines '$out_file1'
   </command>