Merge remote-tracking branch 'origin/develop' into fb_redirectGH1023

Author: cnathe

packages/components/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "@labkey/components",
-  "version": "7.43.1-fb-redirectGH1023.0",
+  "version": "7.45.0",
   "description": "Components, models, actions, and utility functions for LabKey applications and pages",
   "sideEffects": false,
   "files": [

packages/components/package.json

@@ -5,6 +5,22 @@ Components, models, actions, and utility functions for LabKey applications and p
 *Released*: TBD
 - GitHub Issue #1023: Add redirect() helper that uses core-safeRedirect
 
+### version 7.45.0
+*Released*: 25 June 2026
+- GitHub Issue 1234: User management page update to use SiteUsers for inactive users grid
+
+### version 7.44.1
+*Released*: 25 June 2026
+- GH Issue 1191: Don't remove product switch menu from narrow browsers
+- GH Issue 254: Use primary product id to get user menu items instead of current product id.
+
+### version 7.44.0
+*Released*: 25 June 2026
+- Support for filtering the sample lineage graph by sample status
+   - Add metric constant
+   - Add `sampleStatus` field to `LineageNode`
+   - Add `rowId` field to `SampleStatus` model
+
 ### version 7.43.0
 *Released*: 23 June 2026
 - panel.scss: disable margin on h1, h2, etc elements within panel-heading components

packages/components/releaseNotes/components.md

@@ -395,6 +395,7 @@ import {
     getSampleStatus,
     getSampleStatusColor,
     getSampleStatusContainerFilter,
+    getSampleStatusFromSampleRow,
     getSampleStatusType,
     isAllSamplesSchema,
     isSampleOperationPermitted,
@@ -422,7 +423,7 @@ import {
     TestLineageAPIWrapper,
 } from './internal/components/lineage/actions';
 import { withLineage } from './internal/components/lineage/withLineage';
-import { DEFAULT_LINEAGE_DISTANCE } from './internal/components/lineage/constants';
+import { DEFAULT_LINEAGE_DISTANCE, LINEAGE_GRAPH_FILTER_METRIC} from './internal/components/lineage/constants';
 import {
     LINEAGE_DIRECTIONS,
     LINEAGE_GROUPING_GENERATIONS,
@@ -527,6 +528,7 @@ import {
     EntityCreationType,
     INDEPENDENT_SAMPLE_CREATION,
     POOLED_SAMPLE_CREATION,
+    SampleState,
     SampleStateType,
 } from './internal/components/samples/models';
 import { DEFAULT_ALIQUOT_NAMING_PATTERN, SampleTypeModel } from './internal/components/domainproperties/samples/models';
@@ -1407,6 +1409,7 @@ export {
     getSampleStatus,
     getSampleStatusColor,
     getSampleStatusContainerFilter,
+    getSampleStatusFromSampleRow,
     getSampleStatusType,
     getSamplesTestAPIWrapper,
     getSampleTypeDetails,
@@ -1513,6 +1516,7 @@ export {
     LabelHelpTip,
     LabelOverlay,
     LINEAGE_DIRECTIONS,
+    LINEAGE_GRAPH_FILTER_METRIC,
     LINEAGE_GROUPING_GENERATIONS,
     LineageDepthLimitMessage,
     LineageFilter,
@@ -1658,6 +1662,7 @@ export {
     SampleParentDataType,
     SamplePropertyDataType,
     SamplesEditButtonSections,
+    SampleState,
     SampleStateType,
     SampleStatusLegend,
     SampleStatusRenderer,

packages/components/src/index.ts

@@ -17,7 +17,7 @@ import {
     LineageURLResolvers,
 } from './types';
 import { SAMPLE_STATE_COLOR_COLUMN_NAME, SAMPLE_STATE_TYPE_COLUMN_NAME } from '../samples/constants';
-
+export const LINEAGE_GRAPH_FILTER_METRIC = "LineageGraphFilter";
 // Default depth to fetch with the lineage API
 export const DEFAULT_LINEAGE_DISTANCE = 5;
 export const DEFAULT_LINEAGE_DIRECTION = LINEAGE_DIRECTIONS.Children;

packages/components/src/internal/components/lineage/constants.tsx

@@ -2,9 +2,9 @@
  * Copyright (c) 2020-2026 LabKey Corporation. All rights reserved. No portion of this work may be reproduced
  * in any form or by any electronic or mechanical means without written permission from LabKey Corporation.
  */
-import { applyLineageOptions, generateNodesAndEdges, LineageIO, LineageNode, LineageResult } from './models';
+import { applyLineageOptions, generateNodesAndEdges, Lineage, LineageIO, LineageNode, LineageResult } from './models';
 import { DEFAULT_LINEAGE_OPTIONS } from './constants';
-import { LineageFilter } from './types';
+import { LineageFilter, LineageOptions } from './types';
 
 describe('lineage model', () => {
     describe('applyLineageOptions', () => {
@@ -33,6 +33,7 @@ describe('lineage model', () => {
     describe('LineageIO.applyConfig', () => {
         const lineageObj = {
             container: 'container',
+            containerPath: '/container',
             created: '2022-01-20',
             createdBy: 'me',
             modified: '2022-01-21',
@@ -235,13 +236,13 @@ describe('lineage model', () => {
             const parentLsid = 'parent-lsid';
 
             const childNode = LineageNode.create(childLsid, {
-                parents: [{ lsid: parentLsid, name: '&4[0' }],
-                name: '&4[0_1001'
+                parents: [{ lsid: parentLsid }],
+                name: '&4[0_1001',
             });
 
             const parentNode = LineageNode.create(parentLsid, {
-                children: [{ lsid: childLsid, name: '&4[0_1001' }],
-                name: '&4[0'
+                children: [{ lsid: childLsid }],
+                name: '&4[0',
             });
 
             const result = LineageResult.create({
@@ -262,5 +263,87 @@ describe('lineage model', () => {
             expect(nodes[childNode.lsid].level).toEqual(0);
             expect(nodes[childNode.lsid].label).toEqual('＆4[0_1001');
         });
+
+        it('GH Issue #1256: Lineage graph can become disconnected with single aliquot and multiple derivatives', () => {
+            // Parent sample with 2 derived samples and 1 aliquot including derivation runs
+            const result = LineageResult.create({
+                nodes: {
+                    'aliquot-lsid': {
+                        cpasType: 'sample-type-lsid',
+                        materialLineageType: 'Aliquot',
+                        type: 'Sample',
+                        lsid: 'aliquot-lsid',
+                        name: 'Aliquot-1',
+                        expType: 'Material',
+                        parents: [{ lsid: 'aliquot-run-lsid' }],
+                    },
+                    'aliquot-run-lsid': {
+                        cpasType: 'urn:lsid:labkey.org:Protocol:SampleAliquotProtocol',
+                        type: 'Run',
+                        lsid: 'aliquot-run-lsid',
+                        children: [{ lsid: 'aliquot-lsid' }],
+                        name: 'Create aliquot from Parent-1',
+                        expType: 'ExperimentRun',
+                        parents: [{ lsid: 'parent-lsid' }],
+                    },
+                    'derived-one-lsid': {
+                        cpasType: 'sample-type-lsid',
+                        materialLineageType: 'Derivative',
+                        type: 'Sample',
+                        lsid: 'derived-one-lsid',
+                        name: 'Derived-1',
+                        expType: 'Material',
+                        parents: [{ lsid: 'derivation-run-lsid' }],
+                    },
+                    'derived-two-lsid': {
+                        cpasType: 'sample-type-lsid',
+                        materialLineageType: 'Derivative',
+                        type: 'Sample',
+                        lsid: 'derived-two-lsid',
+                        name: 'Derived-2',
+                        expType: 'Material',
+                        parents: [{ lsid: 'derivation-run-lsid' }],
+                    },
+                    'derivation-run-lsid': {
+                        cpasType: 'urn:lsid:labkey.org:Protocol:SampleDerivationProtocol',
+                        type: 'Run',
+                        lsid: 'derivation-run-lsid',
+                        children: [{ lsid: 'derived-two-lsid' }, { lsid: 'derived-one-lsid' }],
+                        name: 'Derive 2 samples from Parent-1',
+                        expType: 'ExperimentRun',
+                        parents: [{ lsid: 'parent-lsid' }],
+                    },
+                    'parent-lsid': {
+                        cpasType: 'sample-type-lsid',
+                        materialLineageType: 'RootMaterial',
+                        type: 'Sample',
+                        lsid: 'parent-lsid',
+                        children: [{ lsid: 'aliquot-run-lsid' }, { lsid: 'derivation-run-lsid' }],
+                        name: 'Parent-1',
+                        expType: 'Material',
+                    },
+                },
+                seed: 'parent-lsid',
+            });
+
+            const options: LineageOptions = {
+                filters: [new LineageFilter('type', ['Sample'])],
+            };
+
+            const lineage = new Lineage({ result });
+            const nodesAndEdges = generateNodesAndEdges(lineage.filterResult(options), options);
+
+            // Runs have been filtered out
+            const expectedNodes = new Set(['aliquot-lsid', 'derived-one-lsid', 'derived-two-lsid', 'parent-lsid']);
+            expect(new Set(Object.keys(nodesAndEdges.nodes))).toEqual(expectedNodes);
+
+            // Previously, this would have only two edges where the edge between the parent and aliquot was missing
+            const expectedEdges = new Set([
+                'parent-lsid||aliquot-lsid',
+                'parent-lsid||derived-one-lsid',
+                'parent-lsid||derived-two-lsid',
+            ]);
+            expect(new Set(Object.keys(nodesAndEdges.edges))).toEqual(expectedEdges);
+        });
     });
 });

packages/components/src/internal/components/lineage/models.test.ts

@@ -291,6 +291,7 @@ export class LineageNode
         steps: undefined,
         type: undefined,
         materialLineageType: undefined,
+        sampleStatus: undefined,
         url: undefined,
 
         // computed properties
@@ -332,6 +333,7 @@ export class LineageNode
     declare steps: List<LineageRunStep>;
     declare type: string;
     declare materialLineageType: string;
+    declare sampleStatus: number;
     declare url: string;
 
     // computed properties
@@ -400,11 +402,11 @@ export class LineageResult extends ImmutableRecord({
         });
     }
 
-    filterIn(field: string, value: string | string[] | undefined): LineageResult {
+    filterIn(field: string, value: string | string[] | number[] | number | undefined): LineageResult {
         return LineageResult._filter(this, field, value, true);
     }
 
-    filterOut(field: string, value: string | string[] | undefined): LineageResult {
+    filterOut(field: string, value: string | string[] | number[] | number | undefined): LineageResult {
         return LineageResult._filter(this, field, value, false);
     }
 
@@ -418,7 +420,7 @@ export class LineageResult extends ImmutableRecord({
     private static _filter(
         result: LineageResult,
         field: string,
-        value: string | string[] | undefined,
+        value: number | number[] | string | string[] | undefined,
         filterIn: boolean
     ): LineageResult {
         if (field === undefined) throw new Error('field must not be undefined');
@@ -457,22 +459,23 @@ export class LineageResult extends ImmutableRecord({
 
     /**
      * When 'filterIn' is true, returns true if the node[field] is equal to the value or any of the array item values.
-     * When value is undefined, it is treated as a wildcard -- any value is allowed as long as the
+     * When value is undefined, it is treated as a wildcard -- any value is allowed as long as the field exists
      *
      * When 'filterIn' is false, returns true if the node[field] is not equal to the value or any of the array item values.
-     * When value is undefined, the node must not have contain a value for the field.
+     * When value is undefined, the node must not contain a value for the field.
      */
     private static _matches(
         node: LineageNode,
         field: string,
-        value: string | string[] | undefined,
+        value: number | number[] | string | string[] | undefined,
         filterIn: boolean
     ): boolean {
         if (filterIn) {
             if (value === undefined) {
                 // true if the field exists on node
                 return node.has(field);
             } else if (Array.isArray(value)) {
+                // @ts-expect-error number or string possible
                 return value.indexOf(node[field]) > -1;
             } else {
                 return node[field] === value;
@@ -482,6 +485,7 @@ export class LineageResult extends ImmutableRecord({
                 // true if the field does not exist on node
                 return !node.has(field);
             } else if (Array.isArray(value)) {
+                // @ts-expect-error number or string possible
                 return value.indexOf(node[field]) === -1;
             } else {
                 return node[field] !== value;
@@ -1137,6 +1141,9 @@ function applyCombineSize(
         combinedLineageNodes.push(
             combineNodes(lsid, aliquotEdges, nodes, options, dir, visEdges, visNodes, nodesInCombinedNode, depth)
         );
+    } else {
+        // GH Issue #1256
+        addEdges(lsid, null, visEdges, List(aliquotEdges), nodesInCombinedNode, dir);
     }
 
     if (nonAliquotEdges.length >= options.grouping.combineSize) {

packages/components/src/internal/components/lineage/models.ts

@@ -42,9 +42,9 @@ export interface LineageGroupingOptions {
 
 export class LineageFilter {
     field: string;
-    value: string[];
+    value: number[] | string[];
 
-    constructor(field: string, value: string[]) {
+    constructor(field: string, value: number[] | string[]) {
         this.field = field;
         this.value = value;
     }

packages/components/src/internal/components/lineage/types.ts

@@ -18,7 +18,7 @@ export interface NavigationAPIWrapper {
         containerId: string,
         containerPath?: string
     ) => Promise<ProductMenuModel>;
-    loadUserMenu: (currentProductId: string, containerPath?: string) => Promise<MenuSectionModel>;
+    loadUserMenu: (productId: string, containerPath?: string) => Promise<MenuSectionModel>;
 }
 
 export class ServerNavigationAPIWrapper implements NavigationAPIWrapper {
@@ -45,9 +45,9 @@ export class ServerNavigationAPIWrapper implements NavigationAPIWrapper {
         }
     };
 
-    loadUserMenu = async (currentProductId: string, containerPath?: string): Promise<MenuSectionModel> => {
+    loadUserMenu = async (productId: string, containerPath?: string): Promise<MenuSectionModel> => {
         try {
-            return await getUserMenuSection(currentProductId, containerPath);
+            return await getUserMenuSection(productId, containerPath);
         } catch (e) {
             return undefined;
         }

packages/components/src/internal/components/navigation/NavigationAPIWrapper.ts

@@ -65,6 +65,7 @@ describe('NavigationBar', () => {
         maxRows: 1,
         markAllNotificationsRead,
         serverActivity: new ServerNotificationModel(),
+        onRead: jest.fn(),
     };
 
     test('default props', async () => {