Merge remote-tracking branch 'origin/production' into issue-4685

Author: CarolineDenis

CHANGELOG.md

@@ -9,6 +9,90 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [7.9.5](https://github.com/specify/specify7/compare/v7.9.4...v7.9.5) (20 May 2024)
+
+This release has for objective to migrated Workbench to React to align it with the rest of the application to ensure consistency and modernising the codebase.
+Workbench functionalities remain unchanged but this release helps improve internal development and maintenance of the workbench going forward. 
+[Workbench Conversion](https://github.com/specify/specify7/pull/4637)
+
+### Added
+
+- **Live Search feature in Workbench**
+
+## [7.9.4](https://github.com/specify/specify7/compare/v7.9.3.1...v7.9.4) (13 May 2024)
+
+### Added
+
+- **Added a visual editor for some app resources**  ([#2796](https://github.com/specify/specify7/pull/2796))
+   - The initial release supports
+      - [Form Definitions](https://discourse.specifysoftware.org/t/editing-forms-in-specify-7/1557)
+      - [Table Formats](https://discourse.specifysoftware.org/t/editing-table-formats-and-aggregations-in-specify-7/1558)
+      - [Table Aggregation](https://discourse.specifysoftware.org/t/editing-table-formats-and-aggregations-in-specify-7/1558)
+   - Visual editors for additional app resources will be added in the future.
+   - Enforce uniqueness requirements for name ([#4164](https://github.com/specify/specify7/pull/4164))
+   - Added query combo box for Specify Users in Export Feed ([#4345](https://github.com/specify/specify7/pull/4345))
+   - Added support for [conditional forms](https://discourse.specifysoftware.org/t/editing-forms-in-specify-7/1557#conditional-rendering-22)
+   - Added a preview for web links, table formats, and table aggregations ([#4343](https://github.com/specify/specify7/pull/4343))
+- Added numerous improvements to distinct queries ([#4596](https://github.com/specify/specify7/pull/4596) – *Requested by University of Kansas, University of Michigan, Commonwealth Scientific and Industrial Research Organisation*)
+   - Added links to records in distinct queries where all columns returned are the same
+   -  Introduced the option to view groups of grouped records in distinct query results 
+   -  Distinct queries can now be exported to CSV
+- Added the ability to display only nodes with associated records in the tree viewer ([#4023](https://github.com/specify/specify7/pull/4023) – Commonwealth Scientific and Industrial Research Organisation)
+- Added the ability to set default values for boolean/checkbox fields in the form definition (#4585 – *Requested by University of Michigan, Commonwealth Scientific and Industrial Research Organisation*
+- Added the ability to import and export WorkBench data set upload plans ([#1363](https://github.com/specify/specify7/issues/1363) – *Requested by Commonwealth Scientific and Industrial Research Organisation and others*)
+- Subforms can now be collapsed ([#3642](https://github.com/specify/specify7/pull/3642) – *Requested by Commonwealth Scientific and Industrial Research Organisation and Agriculture and Agri-Food Canada*)
+- Added a new form element to show a view button next to a query combo box ([#4199](https://github.com/specify/specify7/pull/4199) – *Requested by South African Institute for Aquatic Biodiversity*)
+- Fields in the Schema Config can now be sorted by their visibility status ([#3516](https://github.com/specify/specify7/pull/3516))
+- Added the ability to switch to 'Basic View' and 'Hide Field Mapper' in embedded query dialogs ([#2863](https://github.com/specify/specify7/pull/2863))
+- Added pagination when viewing large lists of resources (record sets, queries, etc.) to improve performance ([#3195](https://github.com/specify/specify7/pull/3195))
+- Added a preference to have records in read-only mode by default requiring the user to press an edit button before changes can be made ([#3553](https://github.com/specify/specify7/pull/3553))
+- Added the ability to hide the plus button in forms ([#3669](https://github.com/specify/specify7/pull/3669) – *Requested by Commonwealth Scientific and Industrial Research Organisation*)
+- Added bulk resolve and bulk return when returning loans ([#4224](https://github.com/specify/specify7/pull/4224) – *Requested by Commonwealth Scientific and Industrial Research Organisation*)
+- Kept the search panel open when modifying XML form ([#4260](https://github.com/specify/specify7/pull/4260))
+- A warning is now displayed if there are no available preparations associated with a catalog number when making an interaction ([#4195](https://github.com/specify/specify7/pull/4195))
+- Added table icons to the WorkBench data sets dialog based on base table in the upload plan ([#4475](https://github.com/specify/specify7/pull/4475))
+- Added frontend business rules for Address `isPrimary` so that it is set by default when adding a new address ([#4443](https://github.com/specify/specify7/pull/4443))
+
+
+### Changed
+- Differentiated list of tables for interactions and data entry ([#4198](https://github.com/specify/specify7/pull/4198))
+- Removed table name before app resource titles ([#4132](https://github.com/specify/specify7/pull/4132))
+- Numeric inputs no longer change on scroll ([#4249](https://github.com/specify/specify7/pull/4249))
+- Disabled gallery icon when there are no attachments on forms ([#4220](https://github.com/specify/specify7/pull/4220))
+- Search preview dialogs no longer display subviews ([#4254](https://github.com/specify/specify7/pull/4254))
+- Improved logic for selecting main tables fields when creating new records from query combo boxes ([#4293](https://github.com/specify/specify7/pull/4293))
+   - Correctly detected main table fields in formatters ([#4516](https://github.com/specify/specify7/pull/4516))
+- Sidebar color preference has been moved and renamed ([#4355](https://github.com/specify/specify7/pull/4355))
+- Displayed disable icon add button instead of link when lowest tree rank ([#4351](https://github.com/specify/specify7/pull/4351))
+- "Use Localized Field Labels" checkbox is now a button ([#4344](https://github.com/specify/specify7/pull/4344))
+- Renamed record merging policy to `/record/merge` ([#4329](https://github.com/specify/specify7/pull/4329))
+- Switched to muted colors for taxon tiles ([#4476](https://github.com/specify/specify7/pull/4476) – *Requested by Virginia Institute of Marine Science*)
+- Miscellaneous Reports dialog improvements ([#4396](https://github.com/specify/specify7/pull/4396))
+- Backend query exports now have user-friendly names  ([#3590](https://github.com/specify/specify7/pull/3590))
+
+### Fixed
+- Fixed an issue where the WorkBench did not always check for  custom uniqueness rules ([#4593](https://github.com/specify/specify7/pull/4593) – *Reported by Commonwealth Scientific and Industrial Research Organisation*)
+- Fixed bug causing incorrect disambiguation behavior in the WorkBench ([#4777](https://github.com/specify/specify7/pull/4777))
+- Made behavior consistent for Reports/Labels across forms and reports dialog, enhanced Report preferences. ([#4299](https://github.com/specify/specify7/pull/4299) – *Reported by Florida Fish and Wildlife Research Institute and Commonwealth Scientific and Industrial Research Organisation*)
+- Fixed an issue that prevented new reports or labels from being created when there was a formatted table in the query ([#4427](https://github.com/specify/specify7/pull/4427) – *Reported by The Hebrew University of Jerusalem, Florida Fish and Wildlife Research Institute, Gothenburg Museum of Natural History, and Oranim College of Education*)
+- Make taxonomic rank properly recompute when the parent changes ([#4462](https://github.com/specify/specify7/pull/4462) – *Reported by Agriculture and Agri-Food Canada*)
+- Added a prompt for a user to define a record set name when creating one ([#4346](https://github.com/specify/specify7/pull/4346))
+- Improved home page load performance ([#4240](https://github.com/specify/specify7/pull/4240))
+- Makes 'Save' button style consistent in Schema Config and Mapper ([#3527](https://github.com/specify/specify7/pull/3527))
+- Make preferences visually read-only for users without proper permissions ([#3551](https://github.com/specify/specify7/pull/3551))
+- Fixed an issue preventing preparations from being added on the Loan form when displayed it was displayed in "form view" ([#3659](https://github.com/specify/specify7/pull/3659))
+- Fixed an issue where a cell or row could be selected multiple times in the WorkBench ([#3675](https://github.com/specify/specify7/pull/3675))
+- Fixed an issue where the WorkBench could not import certain spreadsheets ([#4223](https://github.com/specify/specify7/pull/4223) – *Reported by Royal Botanic Garden Edinburgh*)
+- Refactored date picker and added tests ([#4276](https://github.com/specify/specify7/pull/4276))
+- Fixed spelling mistake in new record set text ([#4317](https://github.com/specify/specify7/pull/4317))
+- The cache is cleared when form edits are made, allowing you to see the latest version ([#4290](https://github.com/specify/specify7/pull/4290))
+- Fixed issues when parsing remote preferences ([#4251](https://github.com/specify/specify7/pull/4251) – *Reported by Museu de Ciències Naturals de Barcelona*)
+- Fix inconsistency with hidden tables in schema and new query lists ([#4357](https://github.com/specify/specify7/pull/4357) – *Reported by Commonwealth Scientific and Industrial Research Organisation*)
+- Made `usertype` get ignored when searching for Common directory app resources to ensure global app resources are applied appropriately ([#4332](https://github.com/specify/specify7/pull/4332))
+- Made minor accessibility improvements ([#4449](https://github.com/specify/specify7/pull/4449))
+- Scoped all front-end requests where needed to prevent resources from returning records from other collections ([#3304](https://github.com/specify/specify7/pull/3304))
+- Fixed WorkBench dialog heading so it displays "Timestamp Uploaded" instead of "Timestamp Modified" ([#4472](https://github.com/specify/specify7/pull/4472))
+
 ## [7.9.3.1](https://github.com/specify/specify7/compare/v7.9.3...v7.9.3.1) (29 January 2024)
 
 This release fixes an issue that could cause an error when viewing an Accession or Repository Agreement form with interaction agents present.

specifyweb/frontend/js_src/css/workbench.css

@@ -77,6 +77,16 @@
   --accent-color: var(--search-result);
 }
 
+/* 
+ * Override default font properties: required for handsontable 10 and above
+ * See: https://github.com/handsontable/handsontable/pull/8681
+ */
+.handsontable {
+  @apply text-inherit;
+  font-family: inherit;
+  font-size: inherit;
+}
+
 /* Handsontable dark mode */
 .handsontable td,
 .htContextMenu table tbody tr td {

specifyweb/frontend/js_src/lib/components/Atoms/Form.tsx

@@ -244,7 +244,7 @@ export const Input = {
     ({ onValueChange, isReadOnly, ...props }) =>
       process.env.NODE_ENV === 'development' &&
       typeof props.step === 'number' &&
-      props.step < 0
+      props.step !== Math.floor(props.step)
         ? error('If step <1 is needed, use Input.Float instead')
         : {
             ...props,
@@ -267,6 +267,7 @@ export const Input = {
       readonly readOnly?: never;
       readonly isReadOnly?: boolean;
       readonly children?: undefined;
+      readonly step?: number | 'any';
     }
   >(
     'Input.Float',
@@ -282,6 +283,7 @@ export const Input = {
         );
         props.onChange?.(event);
       },
+      step: props.step ?? 'any',
       ...withPreventWheel(props.onWheel),
       readOnly: isReadOnly,
     })

specifyweb/frontend/js_src/lib/components/DataModel/__tests__/businessRules.test.ts

@@ -3,6 +3,7 @@ import { renderHook } from '@testing-library/react';
 import { overrideAjax } from '../../../tests/ajax';
 import { mockTime, requireContext } from '../../../tests/helpers';
 import { overwriteReadOnly } from '../../../utils/types';
+import { getPref } from '../../InitialContext/remotePrefs';
 import type { SerializedResource } from '../helperTypes';
 import { getResourceApiUrl } from '../resource';
 import { useSaveBlockers } from '../saveBlockers';
@@ -197,6 +198,18 @@ describe('treeBusinessRules', () => {
     _tableName: 'Taxon',
     id: 3,
     name: 'Acipenser',
+    isAccepted: true,
+    rankId: 180,
+    definition: '/api/specify/taxontreedef/1/',
+    definitionItem: '/api/specify/taxontreedefitem/9/',
+    parent: '/api/specify/taxon/2/',
+  };
+
+  const husoResponse: Partial<SerializedResource<Taxon>> = {
+    _tableName: 'Taxon',
+    id: 6,
+    name: 'Huso',
+    isAccepted: false,
     rankId: 180,
     definition: '/api/specify/taxontreedef/1/',
     definitionItem: '/api/specify/taxontreedefitem/9/',
@@ -207,6 +220,7 @@ describe('treeBusinessRules', () => {
     _tableName: 'Taxon',
     id: 4,
     name: 'oxyrinchus',
+    isAccepted: true,
     rankId: 220,
     definition: '/api/specify/taxontreedef/1/',
     definitionItem: '/api/specify/taxontreedefitem/2/',
@@ -218,6 +232,7 @@ describe('treeBusinessRules', () => {
     id: 5,
     rankId: 230,
     name: 'oxyrinchus',
+    isAccepted: true,
     definition: '/api/specify/taxontreedef/1/',
     definitionItem: '/api/specify/taxontreedefitem/22/',
   };
@@ -250,18 +265,47 @@ describe('treeBusinessRules', () => {
     resource_uri: '/api/specify/taxontreedefitem/2/',
   };
 
+  const subSpeciesResponse: Partial<SerializedResource<TaxonTreeDefItem>> = {
+    id: 22,
+    fullNameSeparator: ' ',
+    isEnforced: false,
+    isInFullName: true,
+    name: 'Subspecies',
+    rankId: 230,
+    title: null,
+    version: 0,
+    parent: '/api/specify/taxontreedefitem/2/',
+    treeDef: '/api/specify/taxontreedef/1/',
+    resource_uri: '/api/specify/taxontreedefitem/22/',
+  };
+
   const oxyrinchusFullNameResponse = 'Acipenser oxyrinchus';
+  const dauricusFullNameResponse = 'Huso dauricus';
 
   overrideAjax('/api/specify/taxon/2/', animaliaResponse);
   overrideAjax('/api/specify/taxon/3/', acipenserResponse);
+  overrideAjax('/api/specify/taxon/6/', husoResponse);
   overrideAjax('/api/specify/taxon/4/', oxyrinchusSpeciesResponse);
   overrideAjax('/api/specify/taxon/5/', oxyrinchusSubSpeciesResponse);
   overrideAjax('/api/specify/taxontreedefitem/9/', genusResponse);
   overrideAjax('/api/specify/taxontreedefitem/2/', speciesResponse);
+  overrideAjax('/api/specify/taxontreedefitem/22/', subSpeciesResponse);
   overrideAjax(
     '/api/specify_tree/taxon/3/predict_fullname/?name=oxyrinchus&treedefitemid=2',
     oxyrinchusFullNameResponse
   );
+  overrideAjax(
+    '/api/specify_tree/taxon/6/predict_fullname/?name=dauricus&treedefitemid=2',
+    dauricusFullNameResponse
+  );
+  overrideAjax('/api/specify/taxon/?limit=1&parent=4&orderby=rankid', {
+    objects: [oxyrinchusSubSpeciesResponse],
+    meta: {
+      limit: 1,
+      offset: 0,
+      total_count: 1,
+    },
+  });
 
   test('fullName being set', async () => {
     const oxyrinchus = new tables.Taxon.Resource({
@@ -306,4 +350,52 @@ describe('treeBusinessRules', () => {
     );
     expect(result.current[0]).toStrictEqual(['Bad tree structure.']);
   });
+  test('saveBlocker on synonymized parent', async () => {
+    const taxon = new tables.Taxon.Resource({
+      name: 'dauricus',
+      parent: '/api/specify/taxon/6/',
+      rankId: 220,
+      definition: '/api/specify/taxontreedef/1/',
+      definitionItem: '/api/specify/taxontreedefitem/2/',
+    });
+
+    await taxon.businessRuleManager?.checkField('parent');
+
+    const { result } = renderHook(() =>
+      useSaveBlockers(taxon, tables.Taxon.getField('parent'))
+    );
+    expect(result.current[0]).toStrictEqual(['Bad tree structure.']);
+
+    await taxon.businessRuleManager?.checkField('integer1');
+
+    const { result: fieldChangeResult } = renderHook(() =>
+      useSaveBlockers(taxon, tables.Taxon.getField('parent'))
+    );
+    expect(fieldChangeResult.current[0]).toStrictEqual(['Bad tree structure.']);
+  });
+  test('saveBlocker not on synonymized parent w/preference', async () => {
+    const remotePrefs = await import('../../InitialContext/remotePrefs');
+    jest
+      .spyOn(remotePrefs, 'getPref')
+      .mockImplementation((key) =>
+        key === 'sp7.allow_adding_child_to_synonymized_parent.Taxon'
+          ? true
+          : getPref(key)
+      );
+
+    const taxon = new tables.Taxon.Resource({
+      name: 'dauricus',
+      parent: '/api/specify/taxon/6/',
+      rankId: 220,
+      definition: '/api/specify/taxontreedef/1/',
+      definitionItem: '/api/specify/taxontreedefitem/2/',
+    });
+
+    await taxon.businessRuleManager?.checkField('parent');
+
+    const { result } = renderHook(() =>
+      useSaveBlockers(taxon, tables.Taxon.getField('parent'))
+    );
+    expect(result.current[0]).toStrictEqual([]);
+  });
 });

specifyweb/frontend/js_src/lib/components/DataModel/businessRules.ts

@@ -8,7 +8,12 @@ import { isTreeResource } from '../InitialContext/treeRanks';
 import type { BusinessRuleDefs } from './businessRuleDefs';
 import { businessRuleDefs } from './businessRuleDefs';
 import { backboneFieldSeparator, djangoLookupSeparator } from './helpers';
-import type { AnySchema, AnyTree, CommonFields } from './helperTypes';
+import type {
+  AnySchema,
+  AnyTree,
+  CommonFields,
+  TableFields,
+} from './helperTypes';
 import type { SpecifyResource } from './legacyTypes';
 import {
   getFieldBlockerKey,
@@ -77,7 +82,7 @@ export class BusinessRuleManager<SCHEMA extends AnySchema> {
       isTreeResource(this.resource as SpecifyResource<AnySchema>)
         ? treeBusinessRules(
             this.resource as SpecifyResource<AnyTree>,
-            processedFieldName
+            processedFieldName as TableFields<AnyTree>
           )
         : Promise.resolve({ isValid: true }),
     ];

specifyweb/frontend/js_src/lib/components/DataModel/treeBusinessRules.ts

@@ -1,13 +1,19 @@
 import { treeText } from '../../localization/tree';
 import { ajax } from '../../utils/ajax';
 import { f } from '../../utils/functools';
+import { getPref } from '../InitialContext/remotePrefs';
+import { fetchPossibleRanks } from '../PickLists/TreeLevelPickList';
 import { formatUrl } from '../Router/queryString';
 import type { BusinessRuleResult } from './businessRules';
-import type { AnyTree, FilterTablesByEndsWith } from './helperTypes';
+import type {
+  AnyTree,
+  FilterTablesByEndsWith,
+  TableFields,
+} from './helperTypes';
 import type { SpecifyResource } from './legacyTypes';
 
 // eslint-disable-next-line unicorn/prevent-abbreviations
-type TreeDefItem<TREE extends AnyTree> =
+export type TreeDefItem<TREE extends AnyTree> =
   FilterTablesByEndsWith<`${TREE['tableName']}TreeDefItem`>;
 
 export const initializeTreeRecord = (
@@ -19,15 +25,33 @@ export const initializeTreeRecord = (
 
 export const treeBusinessRules = async (
   resource: SpecifyResource<AnyTree>,
-  fieldName: string
+  fieldName: TableFields<AnyTree>
 ): Promise<BusinessRuleResult | undefined> =>
   getRelatedTreeTables(resource).then(async ({ parent, definitionItem }) => {
     if (parent === undefined) return undefined;
 
+    const parentDefItem = ((await parent.rgetPromise('definitionItem')) ??
+      undefined) as SpecifyResource<TreeDefItem<AnyTree>> | undefined;
+
+    const possibleRanks =
+      parentDefItem === undefined
+        ? undefined
+        : await fetchPossibleRanks(resource, parentDefItem.get('rankId'));
+
+    const doExpandSynonymActionsPref = getPref(
+      `sp7.allow_adding_child_to_synonymized_parent.${resource.specifyTable.name}`
+    );
+    const isParentSynonym = !parent.get('isAccepted');
+
     const hasBadTreeStrcuture =
       parent.id === resource.id ||
       definitionItem === undefined ||
-      parent.get('rankId') >= definitionItem.get('rankId');
+      (isParentSynonym && !doExpandSynonymActionsPref) ||
+      parent.get('rankId') >= definitionItem.get('rankId') ||
+      (possibleRanks !== undefined &&
+        !possibleRanks
+          .map(({ resource_uri }) => resource_uri)
+          .includes(definitionItem.get('resource_uri')));
 
     if (!hasBadTreeStrcuture && (resource.get('name').length ?? 0) === 0)
       return {
@@ -43,6 +67,7 @@ export const treeBusinessRules = async (
       };
 
     if (
+      hasBadTreeStrcuture ||
       (resource.get('name')?.length ?? 0) === 0 ||
       definitionItem === undefined
     )