Merge branch 'production' into issue-5138

CHANGELOG.md

@@ -9,6 +9,11 @@ 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/).
 
+## [7.9.6.2](https://github.com/specify/specify7/compare/v7.9.6.1...v7.9.6.2) (22 July 2024)
+
+- Fixed an issue that prevented `TimestampModified` from being captured upon saving a record since the `v7.9.6` release ([#5108](https://github.com/specify/specify7/issues/5108) – *Reported by the University of Kansas and Ohio State University*)
+- Fixed an issue that caused large trees to perform slowly or crash the browser due to using too much memory ([#5115](https://github.com/specify/specify7/pull/5115) – *Reported by The Hebrew University of Jerusalem and Royal Botanic Gardens Edinburgh*)
+
 ## [7.9.6.1](https://github.com/specify/specify7/compare/v7.9.6...v7.9.6.1) (9 July 2024)
 
 - Fixes an issue that led to tree definition item separators being trimmed ([#5076](https://github.com/specify/specify7/pull/5076))

requirements.txt

@@ -9,4 +9,3 @@ PyJWT==2.3.0
 django-auth-ldap==1.2.15
 jsonschema==3.2.0
 typing-extensions==4.3.0
-django-model-utils==4.4.0

specifyweb/attachment_gw/models.py

@@ -1,8 +1,4 @@
 from django.db import models
-from django.conf import settings
-from django.db.models.deletion import CASCADE, SET_NULL
-from django.utils import timezone
-from model_utils import FieldTracker
 from functools import partialmethod
 from specifyweb.specify.models import datamodel, custom_save
 from ..workbench.models import Dataset
@@ -15,7 +11,6 @@ class Spattachmentdataset(Dataset):
     class Meta:
         db_table = 'attachmentdataset'
 
-    timestamptracker = FieldTracker(fields=['timestampcreated', 'timestampmodified'])
     save = partialmethod(custom_save)
 
 # from django.apps import apps

specifyweb/frontend/js_src/css/main.css

@@ -150,7 +150,6 @@
   /* Make spinner buttons larger */
   [type='number']:not([readonly], .no-arrows)::-webkit-outer-spin-button,
   [type='number']:not([readonly], .no-arrows)::-webkit-inner-spin-button {
-    -webkit-appearance: inner-spin-button !important;
     @apply absolute right-0 top-0 h-full w-2;
   }
 

specifyweb/frontend/js_src/lib/components/Core/Entrypoint.tsx

@@ -16,8 +16,8 @@ function entrypoint(): void {
 
   interceptLogs();
 
-  console.group('Specify App Starting');
   if (process.env.NODE_ENV === 'production') {
+    console.group('Specify App Starting');
     console.log(
       '%cDocumentation for Developers:\n',
       'font-weight: bold',
@@ -27,7 +27,6 @@ function entrypoint(): void {
   const entrypointName =
     parseDjangoDump<ReturnType<typeof getEntrypointName>>('entrypoint-name') ??
     'main';
-  console.log(entrypointName);
   unlockInitialContext(entrypointName);
 
   globalThis.addEventListener?.('load', () => {

specifyweb/frontend/js_src/lib/components/Errors/interceptLogs.ts

@@ -117,6 +117,13 @@ export function interceptLogs(): void {
       const context = getLogContext();
       const hasContext = Object.keys(context).length > 0;
 
+      // Silencing https://github.com/reactjs/react-modal/issues/808
+      if (
+        args[0] ===
+        "React-Modal: Cannot register modal instance that's already open"
+      )
+        return;
+
       /**
        * If actively redirecting log output, don't print to console
        * (printing object to console prevents garbage collection

specifyweb/frontend/js_src/lib/components/InitialContext/index.ts

@@ -3,10 +3,7 @@
  */
 
 import type { MimeType } from '../../utils/ajax';
-import { f } from '../../utils/functools';
 import { defined } from '../../utils/types';
-import { formatNumber } from '../Atoms/Internationalization';
-import { SECOND } from '../Atoms/timeUnits';
 
 /**
  * This belongs to ./components/toolbar/cachebuster.tsx but was moved here
@@ -56,7 +53,6 @@ export const unlockInitialContext = (entrypoint: typeof entrypointName): void =>
 export const load = async <T>(path: string, mimeType: MimeType): Promise<T> =>
   contextUnlockedPromise.then(async (entrypoint) => {
     if (entrypoint !== 'main') return foreverFetch<T>();
-    const startTime = Date.now();
 
     // Doing async import to avoid a circular dependency
     const { ajax } = await import('../../utils/ajax');
@@ -65,21 +61,7 @@ export const load = async <T>(path: string, mimeType: MimeType): Promise<T> =>
       errorMode: 'visible',
       headers: { Accept: mimeType },
     });
-    const endTime = Date.now();
-    const timePassed = endTime - startTime;
-    // A very crude detection mechanism
-    const isCached = timePassed < 100;
 
-    // So as not to spam the tests
-    if (process.env.NODE_ENV !== 'test')
-      console.log(
-        `${path} %c[${
-          isCached
-            ? 'cached'
-            : `${formatNumber(f.round(timePassed / SECOND, 0.01))}s`
-        }]`,
-        `color: ${isCached ? '#9fa' : '#f99'}`
-      );
     return data;
   });
 

specifyweb/frontend/js_src/lib/components/Permissions/definitions.ts

@@ -1,64 +1,71 @@
 export const tableActions = ['read', 'create', 'update', 'delete'] as const;
 export const collectionAccessResource = '/system/sp7/collection';
 export const operationPolicies = {
-  '/system/sp7/collection': ['access'],
-  '/admin/user/password': ['update'],
   '/admin/user/agents': ['update'],
-  '/admin/user/sp6/is_admin': ['update'],
-  '/record/merge': ['update', 'delete'],
   '/admin/user/invite_link': ['create'],
   '/admin/user/oic_providers': ['read'],
+  '/admin/user/password': ['update'],
   '/admin/user/sp6/collection_access': ['read', 'update'],
-  '/report': ['execute'],
+  '/admin/user/sp6/is_admin': ['update'],
+  '/attachment_import/dataset': [
+    'create',
+    'update',
+    'delete',
+    'upload',
+    'rollback',
+  ],
   '/export/dwca': ['execute'],
   '/export/feed': ['force_update'],
+  '/permissions/library/roles': ['read', 'create', 'update', 'delete'],
   '/permissions/list_admins': ['read'],
   '/permissions/policies/user': ['read', 'update'],
-  '/permissions/user/roles': ['read', 'update'],
   '/permissions/roles': [
     'read',
     'create',
     'update',
     'delete',
     'copy_from_library',
   ],
-  '/permissions/library/roles': ['read', 'create', 'update', 'delete'],
-  '/tree/edit/taxon': ['merge', 'move', 'synonymize', 'desynonymize', 'repair'],
+  '/permissions/user/roles': ['read', 'update'],
+  '/querybuilder/query': [
+    'execute',
+    'export_csv',
+    'export_kml',
+    'create_recordset',
+  ],
+  '/record/merge': ['update', 'delete'],
+  '/report': ['execute'],
+  '/system/sp7/collection': ['access'],
   '/tree/edit/geography': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
   ],
-  '/tree/edit/storage': [
+  '/tree/edit/geologictimeperiod': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
-    'bulk_move',
   ],
-  '/tree/edit/geologictimeperiod': [
+  '/tree/edit/lithostrat': [
     'merge',
     'move',
     'synonymize',
     'desynonymize',
     'repair',
   ],
-  '/tree/edit/lithostrat': [
+  '/tree/edit/storage': [
     'merge',
     'move',
+    'bulk_move',
     'synonymize',
     'desynonymize',
     'repair',
   ],
-  '/querybuilder/query': [
-    'execute',
-    'export_csv',
-    'export_kml',
-    'create_recordset',
-  ],
+  '/tree/edit/taxon': ['merge', 'move', 'synonymize', 'desynonymize', 'repair'],
   '/workbench/dataset': [
     'create',
     'update',
@@ -69,13 +76,6 @@ export const operationPolicies = {
     'transfer',
     'create_recordset',
   ],
-  '/attachment_import/dataset': [
-    'create',
-    'update',
-    'delete',
-    'upload',
-    'rollback',
-  ],
 } as const;
 
 /**

specifyweb/frontend/js_src/lib/components/Permissions/index.ts

@@ -87,7 +87,9 @@ const checkRegistry = async (): Promise<void> =>
       ).then((policies) =>
         sortPolicies(policies) === sortPolicies(operationPolicies)
           ? undefined
-          : error('Front-end has outdated list of operation policies')
+          : error(
+              'Front-end list of operation policies is out of date. To resolve this error, please update "operationPolicies" in specifyweb/frontend/js_src/lib/components/Permissions/definitions.ts based on the response from the http://localhost/permissions/registry/ endpoint'
+            )
       );
 
 export type PermissionsQueryItem = {

specifyweb/frontend/js_src/lib/components/SchemaConfig/Tables.tsx

@@ -16,6 +16,7 @@ import { Link } from '../Atoms/Link';
 import type { SpecifyTable } from '../DataModel/specifyTable';
 import { genericTables } from '../DataModel/tables';
 import type { Tables } from '../DataModel/types';
+import { userInformation } from '../InitialContext/userInformation';
 import { Dialog } from '../Molecules/Dialog';
 import { TableIcon } from '../Molecules/TableIcon';
 import { hasTablePermission } from '../Permissions/helpers';
@@ -86,7 +87,9 @@ export function tablesFilter(
 ): boolean {
   if (selectedTables?.includes(name) === true) return true;
 
-  const isRestricted = overrides.isHidden || overrides.isSystem;
+  const isRestricted = userInformation.isadmin
+    ? overrides.isHidden
+    : overrides.isHidden || overrides.isSystem;
   if (!showHiddenTables && isRestricted) return false;
   const hasAccess = hasTablePermission(name, 'read');
   if (!showNoAccessTables && !hasAccess) return false;

specifyweb/frontend/js_src/lib/components/SchemaConfig/__tests__/Tables.test.ts

@@ -15,7 +15,7 @@ describe('tablesFilter', () => {
     ));
 
   test('showHiddenTables excludes hidden and system', () =>
-    expect(tablesFilter(false, true, true, tables.Institution)).toBe(false));
+    expect(tablesFilter(false, true, true, tables.Institution)).toBe(true));
 
   test('showNoAccessTables excludes table without permission', () => {
     const tablePermissions =

specifyweb/frontend/js_src/lib/components/TreeView/Row.tsx

@@ -1,14 +1,12 @@
 import React from 'react';
 
-import { useAsyncState } from '../../hooks/useAsyncState';
 import { useId } from '../../hooks/useId';
 import { commonText } from '../../localization/common';
 import { treeText } from '../../localization/tree';
 import type { RA } from '../../utils/types';
 import { Button } from '../Atoms/Button';
 import { className } from '../Atoms/className';
 import { icons } from '../Atoms/Icons';
-import { fetchRows } from '../DataModel/collection';
 import type { AnyTree } from '../DataModel/helperTypes';
 import { getPref } from '../InitialContext/remotePrefs';
 import { userPreferences } from '../Preferences/userPreferences';
@@ -150,21 +148,6 @@ export function TreeRow<SCHEMA extends AnyTree>({
   const hasNoChildrenNodes =
     nodeStats?.directCount === 0 && nodeStats.childCount === 0;
 
-  const acceptedChildrenKey = `accepted${treeName.toLowerCase()}`;
-  const [synonymsNames] = useAsyncState(
-    React.useCallback(
-      async () =>
-        fetchRows(treeName as 'Taxon', {
-          fields: { name: ['string'] },
-          limit: 0,
-          [acceptedChildrenKey]: row.nodeId,
-          domainFilter: false,
-        }).then((rows) => rows.map(({ name }) => name)),
-      [acceptedChildrenKey, treeName, row.nodeId]
-    ),
-    false
-  );
-
   return hideEmptyNodes && hasNoChildrenNodes ? null : (
     <li role="treeitem row">
       {ranks.map((rankId) => {
@@ -247,12 +230,11 @@ export function TreeRow<SCHEMA extends AnyTree>({
                       ? treeText.acceptedName({
                           name: row.acceptedName ?? row.acceptedId.toString(),
                         })
-                      : synonymsNames === undefined ||
-                        synonymsNames.length === 0
-                      ? undefined
-                      : treeText.synonyms({
-                          names: synonymsNames.join(', '),
+                      : typeof row.synonyms === 'string'
+                      ? treeText.synonyms({
+                          names: row.synonyms,
                         })
+                      : undefined
                   }
                 >
                   {doIncludeAuthorPref &&

specifyweb/frontend/js_src/lib/components/TreeView/helpers.ts

@@ -24,8 +24,9 @@ export const fetchRows = async (fetchUrl: string) =>
         number,
         number | null,
         string | null,
-        string,
-        number
+        string | null,
+        number,
+        string | null
       ]
     >
   >(fetchUrl, {
@@ -44,6 +45,7 @@ export const fetchRows = async (fetchUrl: string) =>
           acceptedName = undefined,
           author = undefined,
           children,
+          synonyms = undefined,
         ],
         index,
         { length }
@@ -59,6 +61,7 @@ export const fetchRows = async (fetchUrl: string) =>
         author,
         children,
         isLastChild: index + 1 === length,
+        synonyms,
       })
     )
   );

specifyweb/frontend/js_src/lib/components/WbPlanView/CustomSelectElement.tsx

@@ -574,7 +574,7 @@ export function CustomSelectElement({
         aria-haspopup="listbox"
         className={`
           flex min-h-[theme(spacing.8)] min-w-max cursor-pointer
-          items-center gap-1 rounded px-1 text-left
+          items-center gap-1 rounded border border-gray-500 px-1 text-left
           md:min-w-[unset] dark:border-none
           ${
             defaultOption?.isRequired === true

specifyweb/specify/api.py

@@ -414,6 +414,10 @@ def set_field_if_exists(obj, field: str, value) -> None:
     if f.concrete:
         setattr(obj, field, value)
 
+def _maybe_delete(data: Dict[str, Any], to_delete: str):
+    if to_delete in data:
+        del data[to_delete]
+
 def cleanData(model, data: Dict[str, Any], agent) -> Dict[str, Any]:
     """Returns a copy of data with only fields that are part of model, removing
     metadata fields and warning on unexpected extra fields."""
@@ -446,30 +450,18 @@ def cleanData(model, data: Dict[str, Any], agent) -> Dict[str, Any]:
 
     if model is models.Agent:
         # setting user agents is part of the user management system.
-        try:
-            del cleaned['specifyuser']
-        except KeyError:
-            pass
+        _maybe_delete(cleaned, 'specifyuser')
 
     # guid should only be updatable for taxon and geography
     if model not in (models.Taxon, models.Geography):
-        try:
-            del cleaned['guid']
-        except KeyError:
-            pass
+        _maybe_delete(cleaned, 'guid')
 
     # timestampcreated should never be updated.
-    # ... well it is now ¯\_(ツ)_/¯
-    # New requirments are for timestampcreated to be overridable.
-    try:
-        # del cleaned['timestampcreated']
-        pass
-    except KeyError:
-        pass
+    #  _maybe_delete(cleaned, 'timestampcreated')
 
     # Password should be set though the /api/set_password/<id>/ endpoint
-    if model is models.Specifyuser and 'password' in cleaned:
-        del cleaned['password']
+    if model is models.Specifyuser: 
+        _maybe_delete(cleaned, 'password')
 
     return cleaned