Merge branch 'production' into issue-5154-patch

specify · Feb 4, 2025 · a0c1fdf · a0c1fdf
2 parents deef488 + 5139ea6
commit a0c1fdf
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diff --git a/Dockerfile b/Dockerfile
@@ -49,15 +49,15 @@ RUN apt-get update \
         curl \
         git \
         libsasl2-dev \
-        libsasl2-modules-gssapi-mit \
+        libsasl2-modules \
         libldap2-dev \
         libssl-dev \
         libgmp-dev \
         libffi-dev \
         python3.8-venv \
         python3.8-distutils \
         python3.8-dev \
-        default-libmysqlclient-dev \
+        libmariadbclient-dev \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 

diff --git a/requirements.txt b/requirements.txt
@@ -4,8 +4,8 @@ Django==3.2.15
 mysqlclient==2.1.1
 SQLAlchemy==1.2.11
 requests==2.32.2
-pycryptodome==3.15.0
+pycryptodome==3.21.0
 PyJWT==2.3.0
-django-auth-ldap==1.2.15
+django-auth-ldap==1.2.17
 jsonschema==3.2.0
 typing-extensions==4.3.0
diff --git a/specifyweb/frontend/js_src/lib/components/Core/Main.tsx b/specifyweb/frontend/js_src/lib/components/Core/Main.tsx
@@ -25,6 +25,7 @@ export type MenuItem = {
   readonly enabled?: () => Promise<boolean> | boolean;
   readonly icon: JSX.Element;
   readonly name: string;
+  readonly onClick?: () => Promise<void>;
 };
 
 /*

diff --git a/specifyweb/frontend/js_src/lib/components/DataModel/__tests__/businessRules.test.ts b/specifyweb/frontend/js_src/lib/components/DataModel/__tests__/businessRules.test.ts
@@ -131,6 +131,41 @@ describe('Collection Object business rules', () => {
   };
   overrideAjax(otherCollectionObjectTypeUrl, otherCollectionObjectType);
 
+  test('CollectionObject -> determinations: Save blocked when a determination does not belong to COT tree', async () => {
+    const collectionObject = getBaseCollectionObject();
+    collectionObject.set(
+      'collectionObjectType',
+      getResourceApiUrl('CollectionObjectType', 1)
+    );
+
+    const determination =
+      collectionObject.getDependentResource('determinations')?.models[0];
+
+    const { result } = renderHook(() =>
+      useSaveBlockers(determination, tables.Determination.getField('Taxon'))
+    );
+
+    await act(async () => {
+      await collectionObject?.businessRuleManager?.checkField(
+        'collectionObjectType'
+      );
+    });
+    expect(result.current[0]).toStrictEqual([
+      resourcesText.invalidDeterminationTaxon(),
+    ]);
+
+    collectionObject.set(
+      'collectionObjectType',
+      getResourceApiUrl('CollectionObjectType', 2)
+    );
+    await act(async () => {
+      await collectionObject?.businessRuleManager?.checkField(
+        'collectionObjectType'
+      );
+    });
+    expect(result.current[0]).toStrictEqual([]);
+  });
+
   test('CollectionObject -> determinations: New determinations are current by default', async () => {
     const collectionObject = getBaseCollectionObject();
     const determinations =

diff --git a/specifyweb/frontend/js_src/lib/components/DataModel/businessRuleDefs.ts b/specifyweb/frontend/js_src/lib/components/DataModel/businessRuleDefs.ts
@@ -1,10 +1,10 @@
 import { resourcesText } from '../../localization/resources';
-import { f } from '../../utils/functools';
 import type { BusinessRuleResult } from './businessRules';
 import {
   COG_PRIMARY_KEY,
   COG_TOITSELF,
   CURRENT_DETERMINATION_KEY,
+  DETERMINATION_TAXON_KEY,
   ensureSingleCollectionObjectCheck,
   hasNoCurrentDetermination,
 } from './businessRuleUtils';
@@ -19,7 +19,6 @@ import {
   updateLoanPrep,
 } from './interactionBusinessRules';
 import type { SpecifyResource } from './legacyTypes';
-import { fetchResource, idFromUrl } from './resource';
 import { setSaveBlockers } from './saveBlockers';
 import { schema } from './schema';
 import type { Collection } from './specifyTable';
@@ -170,38 +169,31 @@ export const businessRuleDefs: MappedBusinessRuleDefs = {
     },
     fieldChecks: {
       collectionObjectType: async (resource): Promise<undefined> => {
-        /*
-         * TEST: write tests for this
-         *  Delete all determinations
-         */
         const determinations = resource.getDependentResource('determinations');
-        const currentDetermination = determinations?.models.find(
-          (determination) => determination.get('isCurrent')
+        if (determinations === undefined || determinations.models.length === 0)
+          return;
+
+        const taxons = await Promise.all(
+          determinations.models.map(async (det) => det.rgetPromise('taxon'))
         );
+        const coType = await resource.rgetPromise('collectionObjectType');
+        const coTypeTreeDef = coType.get('taxonTreeDef');
 
-        const taxonId = idFromUrl(currentDetermination?.get('taxon') ?? '');
-        const COTypeID = idFromUrl(resource.get('collectionObjectType') ?? '');
-        if (
-          taxonId !== undefined &&
-          COTypeID !== undefined &&
-          currentDetermination !== undefined &&
-          determinations !== undefined
-        )
-          await f
-            .all({
-              fetchedTaxon: fetchResource('Taxon', taxonId),
-              fetchedCOType: fetchResource('CollectionObjectType', COTypeID),
-            })
-            .then(({ fetchedTaxon, fetchedCOType }) => {
-              const taxonTreeDefinition = fetchedTaxon.definition;
-              const COTypeTreeDefinition = fetchedCOType.taxonTreeDef;
+        // Block save when a Determination -> Taxon does not belong to the COType's tree definition
+        determinations.models.forEach((determination, index) => {
+          const taxon = taxons[index];
+          const taxonTreeDef = taxon?.get('definition');
+          const isValid =
+            typeof taxonTreeDef === 'string' && taxonTreeDef === coTypeTreeDef;
+
+          setSaveBlockers(
+            determination,
+            determination.specifyTable.field.taxon,
+            isValid ? [] : [resourcesText.invalidDeterminationTaxon()],
+            DETERMINATION_TAXON_KEY
+          );
+        });
 
-              if (taxonTreeDefinition !== COTypeTreeDefinition)
-                resource.set('determinations', []);
-            })
-            .catch((error) => {
-              console.error('Error fetching resources:', error);
-            });
         return undefined;
       },
     },

diff --git a/specifyweb/frontend/js_src/lib/components/DataModel/businessRuleUtils.ts b/specifyweb/frontend/js_src/lib/components/DataModel/businessRuleUtils.ts
@@ -7,6 +7,7 @@ export const CURRENT_DETERMINATION_KEY = 'determination-isCurrent';
 export const COG_TOITSELF = 'cog-toItself';
 export const PARENTCOG_KEY = 'cog-parentCog';
 export const COG_PRIMARY_KEY = 'cog-isPrimary';
+export const DETERMINATION_TAXON_KEY = 'determination-Taxon';
 
 /**
  *

diff --git a/specifyweb/frontend/js_src/lib/components/Header/UserTools.tsx b/specifyweb/frontend/js_src/lib/components/Header/UserTools.tsx
@@ -140,10 +140,11 @@ function UserToolsColumn({
         <div className="flex flex-col gap-2" key={groupName}>
           <H3>{groupName}</H3>
           <Ul className="flex flex-col gap-1">
-            {userTools.map(({ title, url, icon }) => {
+            {userTools.map(({ title, url, icon, onClick }) => {
               const isExternalLink = isExternalUrl(url);
               // Make links to another entrypoint trigger page reload
               const LinkComponent = isExternalLink ? Link.NewTab : Link.Default;
+
               return (
                 <li key={url}>
                   <LinkComponent
@@ -154,6 +155,7 @@ function UserToolsColumn({
                         : undefined
                     }
                     href={url}
+                    onClick={onClick}
                   >
                     {icon}
                     {title}

diff --git a/specifyweb/frontend/js_src/lib/components/Header/userToolDefinitions.ts b/specifyweb/frontend/js_src/lib/components/Header/userToolDefinitions.ts
@@ -19,6 +19,7 @@ import {
   hasTablePermission,
   hasToolPermission,
 } from '../Permissions/helpers';
+import { clearAllCache } from '../RouterCommands/CacheBuster';
 import { filterMenuItems } from './menuItemProcessing';
 
 const rawUserTools = ensure<IR<IR<Omit<MenuItem, 'name'>>>>()({
@@ -28,6 +29,14 @@ const rawUserTools = ensure<IR<IR<Omit<MenuItem, 'name'>>>>()({
       url: '/accounts/logout/',
       icon: icons.logout,
       enabled: () => userInformation.isauthenticated,
+      onClick: async () =>
+        clearAllCache()
+          .then(() => {
+            console.log('Cache cleared successfully.');
+          })
+          .catch((error) => {
+            console.error('Error occurred during cache clearing:', error);
+          }),
     },
     changePassword: {
       title: userText.changePassword(),

diff --git a/specifyweb/frontend/js_src/lib/components/Preferences/UserDefinitions.tsx b/specifyweb/frontend/js_src/lib/components/Preferences/UserDefinitions.tsx
@@ -64,7 +64,8 @@ const isDarkMode = ({
   isRedirecting,
 }: PreferencesVisibilityContext): boolean => isDarkMode || isRedirecting;
 
-const altKeyName = globalThis.navigator?.appVersion.includes('Mac')
+// Navigator may not be defined in some environments, like non-browser environments
+const altKeyName = typeof navigator !== 'undefined' && navigator?.userAgent?.includes('Mac')
   ? 'Option'
   : 'Alt';
 

diff --git a/specifyweb/frontend/js_src/lib/components/QueryComboBox/helpers.ts b/specifyweb/frontend/js_src/lib/components/QueryComboBox/helpers.ts
@@ -147,7 +147,7 @@ export function getQueryComboBoxConditions({
    * Filter values by tree definition if provided through context.
    * Used for filtering Taxon values by COT tree definition.
    */
-  if (treeDefinition !== undefined) {
+  if (treeDefinition !== undefined && relatedTable === tables.Taxon) {
     fields.push(
       QueryFieldSpec.fromPath(tables.Taxon.name, ['definition', 'id'])
         .toSpQueryField()

diff --git a/specifyweb/frontend/js_src/lib/components/QueryComboBox/index.tsx b/specifyweb/frontend/js_src/lib/components/QueryComboBox/index.tsx
@@ -264,25 +264,29 @@ export function QueryComboBox({
     (typeof typeSearch === 'object' ? typeSearch?.table : undefined) ??
     field.relatedTable;
 
-  const [fetchedTreeDefinition] = useAsyncState(
-    React.useCallback(
-      async () =>
-        resource?.specifyTable === tables.Determination &&
-        resource.collection?.related?.specifyTable === tables.CollectionObject
-          ? (resource.collection?.related as SpecifyResource<CollectionObject>)
-              .rgetPromise('collectionObjectType')
-              .then(
-                (
-                  collectionObjectType:
-                    | SpecifyResource<CollectionObjectType>
-                    | undefined
-                ) => collectionObjectType?.get('taxonTreeDef')
-              )
-          : undefined,
-      [resource, resource?.collection?.related?.get('collectionObjectType')]
-    ),
-    false
-  );
+    const [fetchedTreeDefinition] = useAsyncState(
+      React.useCallback(async () => {
+        if (resource?.specifyTable === tables.Determination) {
+          return resource.collection?.related?.specifyTable === tables.CollectionObject
+            ? (resource.collection?.related as SpecifyResource<CollectionObject>)
+                .rgetPromise('collectionObjectType')
+                .then(
+                  (
+                    collectionObjectType:
+                      | SpecifyResource<CollectionObjectType>
+                      | undefined
+                  ) => collectionObjectType?.get('taxonTreeDef')
+                )
+            : undefined;
+        } else if (resource?.specifyTable === tables.Taxon) {
+          const definition = resource.get('definition')
+          const parentDefinition = (resource?.independentResources?.parent as SpecifyResource<AnySchema>)?.get?.('definition');
+          return definition || parentDefinition;
+      }
+        return undefined;
+      }, [resource, resource?.collection?.related?.get('collectionObjectType')]),
+      false
+    );
 
   // Tree Definition passed by a parent QCBX in the component tree
   const parentTreeDefinition = React.useContext(TreeDefinitionContext);
@@ -550,6 +554,10 @@ export function QueryComboBox({
                                         : fieldName === 'taxonTreeDefId'
                                           ? {
                                               field: 'definition',
+                                              queryBuilderFieldPath: [
+                                                'definition',
+                                                'id',
+                                              ],
                                               isRelationship: true,
                                               operation: 'in',
                                               isNot: false,

diff --git a/specifyweb/frontend/js_src/lib/components/RouterCommands/SwitchCollection.tsx b/specifyweb/frontend/js_src/lib/components/RouterCommands/SwitchCollection.tsx
@@ -7,6 +7,7 @@ import { useAsyncState } from '../../hooks/useAsyncState';
 import { toLocalUrl } from '../../utils/ajax/helpers';
 import { ping } from '../../utils/ajax/ping';
 import { formatUrl } from '../Router/queryString';
+import { clearAllCache } from './CacheBuster';
 
 export const switchCollection = (
   navigate: SafeNavigateFunction,
@@ -40,7 +41,9 @@ export function SwitchCollectionCommand(): null {
           method: 'POST',
           body: collectionId!.toString(),
           errorMode: 'dismissible',
-        }).then(() => globalThis.location.replace(nextUrl)),
+        })
+        .then(clearAllCache)
+        .then(() => globalThis.location.replace(nextUrl)),
       [collectionId, nextUrl]
     ),
     true

diff --git a/specifyweb/frontend/js_src/lib/components/SearchDialog/index.tsx b/specifyweb/frontend/js_src/lib/components/SearchDialog/index.tsx
@@ -35,13 +35,15 @@ import type { QueryFieldFilter } from '../QueryBuilder/FieldFilter';
 import { queryFieldFilters } from '../QueryBuilder/FieldFilter';
 import { QueryFieldSpec } from '../QueryBuilder/fieldSpec';
 import { QueryBuilder } from '../QueryBuilder/Wrapped';
+import type { MappingPath } from '../WbPlanView/Mapper';
 import { queryCbxExtendedSearch } from './helpers';
 import { SelectRecordSets } from './SelectRecordSet';
 
 const resourceLimit = 100;
 
 export type QueryComboBoxFilter<SCHEMA extends AnySchema> = {
   readonly field: string & (keyof CommonFields | keyof SCHEMA['fields']);
+  readonly queryBuilderFieldPath?: MappingPath;
   readonly isRelationship: boolean;
   readonly isNot: boolean;
   readonly operation: QueryFieldFilter & ('between' | 'in' | 'less');
@@ -156,7 +158,6 @@ function testFilter<SCHEMA extends AnySchema>(
         ? // Cast numbers to strings
           values.some((value) => {
             const fieldValue = resource.get(field);
-
             return isRelationship
               ? value == strictIdFromUrl(fieldValue!).toString()
               : value == fieldValue;
@@ -395,8 +396,8 @@ const toQueryFields = <SCHEMA extends AnySchema>(
   table: SpecifyTable<SCHEMA>,
   filters: RA<QueryComboBoxFilter<SCHEMA>>
 ): RA<SpecifyResource<SpQueryField>> =>
-  filters.map(({ field, operation, isNot, value }) =>
-    QueryFieldSpec.fromPath(table.name, [field])
+  filters.map(({ field, queryBuilderFieldPath, operation, isNot, value }) =>
+    QueryFieldSpec.fromPath(table.name, queryBuilderFieldPath ?? [field])
       .toSpQueryField()
       .set('operStart', queryFieldFilters[operation].id)
       .set('isNot', isNot)

diff --git a/specifyweb/frontend/js_src/lib/localization/common.ts b/specifyweb/frontend/js_src/lib/localization/common.ts
@@ -736,6 +736,7 @@ export const commonText = createDictionary({
   },
   zoom: {
     'en-us': 'Zoom',
+    'fr-fr': 'Zoom',
   },
   unzoom: {
     'en-us': 'Unzoom',

diff --git a/specifyweb/frontend/js_src/lib/localization/resources.ts b/specifyweb/frontend/js_src/lib/localization/resources.ts
@@ -846,4 +846,8 @@ export const resourcesText = createDictionary({
     'en-us':
       'A Consolidated Collection Object Group must have a primary Collection Object child',
   },
+  invalidDeterminationTaxon: {
+    'en-us':
+      'Determination does not belong to the taxon tree associated with the Collection Object Type',
+  },
 } as const);