[Lens] Mute visualization modifier badge if layer has only manual annotations (#167483)

## Summary

Fixes #167408 

This PR reduces the amount of "visualization modifiers" in the specific
case where ALL annotations in a layer are manual.
The `Ignore global filters` will still be shown if at least one
query-based annotation is defined in the layer.


### Checklist

Delete any items that are not applicable to this PR.

- [x] [Unit or functional
tests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)
were updated or added to match the most common scenarios

---------

Co-authored-by: Stratoula Kalafateli <efstratia.kalafateli@elastic.co>

x-pack/plugins/lens/public/visualizations/xy/visualization.test.tsx

@@ -731,12 +731,14 @@ describe('xy_visualization', () => {
           },
         };
       });
+
       it('when there is no date histogram annotation layer is disabled', () => {
         const supportedAnnotationLayer = xyVisualization
           .getSupportedLayers(exampleState())
           .find((a) => a.type === 'annotations');
         expect(supportedAnnotationLayer?.disabled).toBeTruthy();
       });
+
       it('for data with date histogram annotation layer is enabled and calculates initial dimensions', () => {
         const supportedAnnotationLayer = xyVisualization
           .getSupportedLayers(exampleState(), frame)
@@ -3216,6 +3218,34 @@ describe('xy_visualization', () => {
     });
 
     describe('info', () => {
+      function createStateWithAnnotationProps(annotation: Partial<EventAnnotationConfig>) {
+        return {
+          layers: [
+            {
+              layerId: 'first',
+              layerType: layerTypes.DATA,
+              seriesType: 'area',
+              splitAccessor: undefined,
+              xAccessor: DATE_HISTORGRAM_COLUMN_ID,
+              accessors: ['b'],
+            },
+            {
+              layerId: 'layerId',
+              layerType: 'annotations',
+              indexPatternId: 'first',
+              annotations: [
+                {
+                  label: 'Event',
+                  id: '1',
+                  type: 'query',
+                  timeField: 'start_date',
+                  ...annotation,
+                },
+              ],
+            },
+          ],
+        } as XYState;
+      }
       function getFrameMock() {
         const datasourceMock = createMockDatasource('testDatasource');
         datasourceMock.publicAPIMock.getOperationForColumnId.mockImplementation((id) =>
@@ -3239,21 +3269,47 @@ describe('xy_visualization', () => {
         });
       }
 
-      it('should return an info message if annotation layer is ignoring the global filters', () => {
-        const initialState = exampleState();
+      it('should not return an info message if annotation layer is ignoring the global filters but contains only manual annotations', () => {
+        const initialState = createStateWithAnnotationProps({});
         const state: State = {
           ...initialState,
           layers: [
-            ...initialState.layers,
+            // replace the existing annotation layers with a new one
+            ...initialState.layers.filter(({ layerType }) => layerType !== layerTypes.ANNOTATIONS),
             {
               layerId: 'annotation',
               layerType: layerTypes.ANNOTATIONS,
-              annotations: [exampleAnnotation2],
+              annotations: [exampleAnnotation2, { ...exampleAnnotation2, id: 'an3' }],
               ignoreGlobalFilters: true,
               indexPatternId: 'myIndexPattern',
             },
           ],
         };
+        expect(xyVisualization.getUserMessages!(state, { frame: getFrameMock() })).toHaveLength(0);
+      });
+
+      it("should return an info message if the annotation layer is ignoring filters and there's at least a query annotation", () => {
+        const state = createStateWithAnnotationProps({
+          filter: {
+            language: 'kuery',
+            query: 'agent.keyword: *',
+            type: 'kibana_query',
+          },
+          id: 'newColId',
+          key: {
+            type: 'point_in_time',
+          },
+          label: 'agent.keyword: *',
+          timeField: 'timestamp',
+          type: 'query',
+        });
+
+        const annotationLayer = state.layers.find(
+          ({ layerType }) => layerType === layerTypes.ANNOTATIONS
+        )! as XYAnnotationLayerConfig;
+        annotationLayer.ignoreGlobalFilters = true;
+        annotationLayer.annotations.push(exampleAnnotation2);
+
         expect(xyVisualization.getUserMessages!(state, { frame: getFrameMock() })).toContainEqual(
           expect.objectContaining({
             displayLocations: [{ id: 'embeddableBadge' }],
@@ -3264,6 +3320,30 @@ describe('xy_visualization', () => {
           })
         );
       });
+
+      it('should not return an info message if annotation layer is not ignoring the global filters', () => {
+        const state = createStateWithAnnotationProps({
+          filter: {
+            language: 'kuery',
+            query: 'agent.keyword: *',
+            type: 'kibana_query',
+          },
+          id: 'newColId',
+          key: {
+            type: 'point_in_time',
+          },
+          label: 'agent.keyword: *',
+          timeField: 'timestamp',
+          type: 'query',
+        });
+
+        const annotationLayer = state.layers.find(
+          ({ layerType }) => layerType === layerTypes.ANNOTATIONS
+        )! as XYAnnotationLayerConfig;
+        annotationLayer.ignoreGlobalFilters = false;
+        annotationLayer.annotations.push(exampleAnnotation2);
+        expect(xyVisualization.getUserMessages!(state, { frame: getFrameMock() })).toHaveLength(0);
+      });
     });
   });
 

x-pack/plugins/lens/public/visualizations/xy/visualization.tsx

@@ -1149,7 +1149,10 @@ function getNotifiableFeatures(
   fieldFormats: FieldFormatsStart
 ): UserMessage[] {
   const annotationsWithIgnoreFlag = getAnnotationsLayers(state.layers).filter(
-    (layer) => layer.ignoreGlobalFilters
+    (layer) =>
+      layer.ignoreGlobalFilters &&
+      // If all annotations are manual, do not report it
+      layer.annotations.some((annotation) => annotation.type !== 'manual')
   );
   if (!annotationsWithIgnoreFlag.length) {
     return [];

x-pack/test/functional/apps/lens/group2/layer_actions.ts

@@ -12,6 +12,7 @@ export default function ({ getService, getPageObjects }: FtrProviderContext) {
   const PageObjects = getPageObjects(['visualize', 'lens', 'common', 'header']);
   const find = getService('find');
   const testSubjects = getService('testSubjects');
+  const retry = getService('retry');
 
   describe('lens layer actions tests', () => {
     it('should allow creation of lens xy chart', async () => {
@@ -239,6 +240,21 @@ export default function ({ getService, getPageObjects }: FtrProviderContext) {
       // by default annotations ignore global filters
       await PageObjects.lens.createLayer('annotations');
 
+      await testSubjects.click('lns-layerPanel-2 > lnsXY_xAnnotationsPanel > lns-dimensionTrigger');
+
+      await testSubjects.click('lnsXY_annotation_query');
+
+      await retry.try(async () => {
+        if (!(await testSubjects.exists('annotation-query-based-query-input'))) {
+          await testSubjects.setValue('annotation-query-based-query-input', '*', {
+            clearWithKeyboard: true,
+            typeCharByChar: true,
+          });
+        }
+      });
+
+      await PageObjects.lens.closeDimensionEditor();
+
       await PageObjects.lens.save('sampledVisualization', false, true, false, 'new');
 
       // now check for the bottom-left badge