Fix schema override

specifyweb/frontend/js_src/lib/components/SetupTool/SetupForm.tsx

@@ -25,7 +25,12 @@ import type {
 } from '../TreeView/CreateTree';
 import { PopulatedTreeList } from '../TreeView/CreateTree';
 import type { FieldConfig, ResourceConfig } from './setupResources';
-import { disciplineTypeOptions, FIELD_MAX_LENGTH, resources,stepOrder } from './setupResources';
+import {
+  disciplineTypeOptions,
+  FIELD_MAX_LENGTH,
+  resources,
+  stepOrder,
+} from './setupResources';
 import type { ResourceFormData } from './types';
 
 function getFormValue(
@@ -142,15 +147,20 @@ export function renderFormFieldFactory({
 
     const verticalSpacing = width !== undefined && width < 2 ? '-mb-2' : 'mb-2';
 
-    const disciplineTypeValue = getFormValue(formData, stepOrder.indexOf('discipline'), 'type');
+    const disciplineTypeValue = getFormValue(
+      formData,
+      stepOrder.indexOf('discipline'),
+      'type'
+    );
     const isDisciplineNameDisabled =
       resources[currentStep].resourceName === 'discipline' &&
       fieldName === 'name' &&
       (disciplineTypeValue === undefined || disciplineTypeValue === '');
 
     const isRowEnableToggle = name === 'include';
-    const isRowEnabled =
-      Boolean(getFormValue(formData, currentStep, `${parentName}.include`));
+    const isRowEnabled = Boolean(
+      getFormValue(formData, currentStep, `${parentName}.include`)
+    );
 
     const taxonTreeAvailable =
       Array.isArray(treeOptions) &&
@@ -177,9 +187,7 @@ export function renderFormFieldFactory({
                     getFormValue(formData, currentStep, fieldName)
                   )}
                   disabled={
-                    inTable
-                      ? !isRowEnabled && !isRowEnableToggle
-                      : false
+                    inTable ? !isRowEnabled && !isRowEnableToggle : false
                   }
                   id={fieldName}
                   name={fieldName}
@@ -325,7 +333,7 @@ export function renderFormFieldFactory({
                   <PopulatedTreeList
                     discipline={disciplineTypeValue as string | undefined}
                     handleClick={(
-                      resource: TaxonFileDefaultDefinition,
+                      resource: TaxonFileDefaultDefinition
                     ): void => {
                       handleChange(fieldName, resource);
                       handleChange('preload', true);
@@ -351,10 +359,14 @@ export function renderFormFieldFactory({
               value={getFormValue(formData, currentStep, fieldName) ?? ''}
               onChange={({ target }) => {
                 // Only allow unique discipline names
-                if (resources[currentStep].resourceName === 'discipline' && fieldName === 'name') {
+                if (
+                  resources[currentStep].resourceName === 'discipline' &&
+                  fieldName === 'name'
+                ) {
                   const value = (target.value ?? '').trim();
-                  const existingDisciplines = institutionData.children.flatMap(division =>
-                    division.children.map(discipline => discipline.name)
+                  const existingDisciplines = institutionData.children.flatMap(
+                    (division) =>
+                      division.children.map((discipline) => discipline.name)
                   );
                   const isUsed = existingDisciplines.includes(value);
                   target.setCustomValidity(
@@ -441,7 +453,7 @@ export function updateSetupFormData(
   name: string,
   newValue: LocalizedString | TaxonFileDefaultDefinition | boolean,
   currentStep: number,
-  institutionData?: InstitutionData,
+  institutionData?: InstitutionData
 ): void {
   setFormData((previous: ResourceFormData) => {
     const resourceName = resources[currentStep].resourceName;
@@ -457,10 +469,15 @@ export function updateSetupFormData(
         (option) => option.value === newValue
       );
       if (matchingType) {
-        const existingDisciplines = institutionData ? institutionData.children.flatMap(division =>
-          division.children.map(discipline => discipline.name)
-        ) : [];
-        const disciplineName = getUniqueName(matchingType.label, existingDisciplines);
+        const existingDisciplines = institutionData
+          ? institutionData.children.flatMap((division) =>
+              division.children.map((discipline) => discipline.name)
+            )
+          : [];
+        const disciplineName = getUniqueName(
+          matchingType.label,
+          existingDisciplines
+        );
         updates.name = matchingType ? disciplineName : '';
       }
 
@@ -485,4 +502,4 @@ export function updateSetupFormData(
       [resourceName]: updates,
     };
   });
-}
+}

specifyweb/frontend/js_src/lib/components/SystemConfigurationTool/Hierarchy.tsx

@@ -28,6 +28,7 @@ import { tables } from '../DataModel/tables';
 import { getSystemInfo } from '../InitialContext/systemInfo';
 import { Dialog, LoadingScreen } from '../Molecules/Dialog';
 import { ResourceLink } from '../Molecules/ResourceLink';
+import { hasTablePermission } from '../Permissions/helpers';
 import { tableLabel } from '../Preferences/UserDefinitions';
 import {
   applyFormDefaults,
@@ -40,7 +41,6 @@ import { nestAllResources } from '../SetupTool/utils';
 import type { TaxonFileDefaultDefinition } from '../TreeView/CreateTree';
 import { CollapsibleSection } from './CollapsibleSection';
 import type { InstitutionData } from './Utils';
-import { hasTablePermission } from '../Permissions/helpers';
 
 type HierarchyNodeKind =
   | 'collection'

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

@@ -209,8 +209,8 @@ export function ImportTree<SCHEMA extends AnyTree>({
   readonly tableName: SCHEMA['tableName'];
   readonly treeDefId: number;
   readonly treeDefinitionItems: RA<
-      SerializedResource<FilterTablesByEndsWith<'TreeDefItem'>>
-    >;
+    SerializedResource<FilterTablesByEndsWith<'TreeDefItem'>>
+  >;
   readonly buttonLabel?: LocalizedString;
   readonly buttonClassName?: string;
 }): JSX.Element {
@@ -222,9 +222,14 @@ export function ImportTree<SCHEMA extends AnyTree>({
     string | undefined
   >(undefined);
 
-  const [missingTreeRanks, setMissingTreeRanks] = React.useState<RA<string> | undefined>(undefined);
-  const [isMissingTreeRanks, setIsMissingTreeRanks] = React.useState<boolean>(false);
-  const [selectedPopulatedTree, setSelectedPopulatedTree] = React.useState<TaxonFileDefaultDefinition | undefined>(undefined);
+  const [missingTreeRanks, setMissingTreeRanks] = React.useState<
+    RA<string> | undefined
+  >(undefined);
+  const [isMissingTreeRanks, setIsMissingTreeRanks] =
+    React.useState<boolean>(false);
+  const [selectedPopulatedTree, setSelectedPopulatedTree] = React.useState<
+    TaxonFileDefaultDefinition | undefined
+  >(undefined);
 
   const connectedCollection = getSystemInfo().collection;
 
@@ -240,15 +245,20 @@ export function ImportTree<SCHEMA extends AnyTree>({
           method: 'POST',
           headers: { Accept: 'application/json' },
           body: {
-            mappingUrl: resource.mappingFile
-          }
+            mappingUrl: resource.mappingFile,
+          },
         });
         if (response.status === Http.OK && response.data) {
-          const mappingRankNames = response.data.ranks.map((rank: any) => rank.name);
-          const existingNames = new Set(treeDefinitionItems.map((item) => item.name));
+          const mappingRankNames = response.data.ranks.map(
+            (rank: any) => rank.name
+          );
+          const existingNames = new Set(
+            treeDefinitionItems.map((item) => item.name)
+          );
 
-          const missing = mappingRankNames
-            .filter((rankName: string) => !existingNames.has(rankName));
+          const missing = mappingRankNames.filter(
+            (rankName: string) => !existingNames.has(rankName)
+          );
 
           if (missing.length > 0) {
             setSelectedPopulatedTree(resource);
@@ -323,9 +333,7 @@ export function ImportTree<SCHEMA extends AnyTree>({
       {isActive === 1 ? (
         <Dialog
           buttons={
-            <Button.DialogClose>
-              {commonText.cancel()}
-            </Button.DialogClose>
+            <Button.DialogClose>{commonText.cancel()}</Button.DialogClose>
           }
           header={commonText.import()}
           onClose={() => setIsActive(0)}
@@ -368,7 +376,7 @@ async function startTreeCreation(
   treeName: string,
   treeDefId: number | undefined,
   createMissingRanks: boolean | undefined,
-  onSuccess: (taskId: string | undefined) => void,
+  onSuccess: (taskId: string | undefined) => void
 ): Promise<void> {
   return ajax<TreeCreationInfo>('/trees/create_default_tree/', {
     method: 'POST',
@@ -389,10 +397,7 @@ async function startTreeCreation(
         console.log(`${treeName} tree created successfully:`, data);
       } else if (status === Http.ACCEPTED) {
         // Tree is being created in the background.
-        console.log(
-          `${treeName} tree creation started successfully:`,
-          data
-        );
+        console.log(`${treeName} tree creation started successfully:`, data);
         onSuccess(data.task_id);
       }
     })
@@ -488,34 +493,26 @@ export function MissingTreeRanksDialog({
     <Dialog
       buttons={
         <>
-          <Button.DialogClose>
-            {commonText.close()}
-          </Button.DialogClose>
+          <Button.DialogClose>{commonText.close()}</Button.DialogClose>
           <Button.Secondary onClick={handleNo}>
             {commonText.no()}
           </Button.Secondary>
-          <Button.Info onClick={handleYes}>
-            {queryText.yes()}
-          </Button.Info>
+          <Button.Info onClick={handleYes}>{queryText.yes()}</Button.Info>
         </>
       }
       header={treeText.missingRanks()}
       onClose={onClose}
     >
       <div className="mb-4 flex flex-col gap-4">
-        <section>
-          {treeText.missingRanksDescription()}
-        </section>
+        <section>{treeText.missingRanksDescription()}</section>
         <section>
           <ul className="ml-4">
             {missingTreeRanks && missingTreeRanks.length > 0
               ? missingTreeRanks.map((rank) => <li key={rank}>{rank}</li>)
               : null}
           </ul>
         </section>
-        <section>
-          {treeText.createMissingRanks()}
-        </section>
+        <section>{treeText.createMissingRanks()}</section>
       </div>
     </Dialog>
   );

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

@@ -22,6 +22,7 @@ import { idFromUrl } from '../DataModel/resource';
 import { deserializeResource } from '../DataModel/serializers';
 import { softError } from '../Errors/assert';
 import { ResourceView } from '../Forms/ResourceView';
+import { userInformation } from '../InitialContext/userInformation';
 import { hasTablePermission } from '../Permissions/helpers';
 import { useHighContrast } from '../Preferences/Hooks';
 import { userPreferences } from '../Preferences/userPreferences';
@@ -31,7 +32,6 @@ import { ImportTree } from './CreateTree';
 import type { Conformations, Row, Stats } from './helpers';
 import { fetchStats } from './helpers';
 import { TreeRow } from './Row';
-import { userInformation } from '../InitialContext/userInformation';
 
 const treeToPref = {
   Geography: 'geography',
@@ -168,10 +168,7 @@ export function Tree<
           stop();
           globalThis.location.reload();
           return;
-        } else if (
-          oldTreeCreationProgress === undefined &&
-          !data.active
-        ) {
+        } else if (oldTreeCreationProgress === undefined && !data.active) {
           // Tree was already complete
           stop();
         }
@@ -318,7 +315,8 @@ export function Tree<
                     ?.slice(1) as Conformations
                 }
                 focusPath={
-                  (focusPath[0] === 0 && index === 0) || focusPath[0] === row.nodeId
+                  (focusPath[0] === 0 && index === 0) ||
+                  focusPath[0] === row.nodeId
                     ? focusPath.slice(1)
                     : undefined
                 }
@@ -342,13 +340,16 @@ export function Tree<
                     setFocusPath([rows[index - 1].nodeId]);
                   else if (action === 'previous' || action === 'parent')
                     setFocusPath([]);
-                  else if (action === 'focusPrevious') focusRef.current?.focus();
-                  else if (action === 'focusNext') searchBoxRef.current?.focus();
+                  else if (action === 'focusPrevious')
+                    focusRef.current?.focus();
+                  else if (action === 'focusNext')
+                    searchBoxRef.current?.focus();
                   return undefined;
                 }}
                 onChangeConformation={(newConformation): void =>
                   setConformation([
-                    ...(conformation?.filter(([id]) => id !== row.nodeId) ?? []),
+                    ...(conformation?.filter(([id]) => id !== row.nodeId) ??
+                      []),
                     ...(typeof newConformation === 'object'
                       ? ([[row.nodeId, ...newConformation]] as const)
                       : []),

specifyweb/frontend/js_src/lib/localization/tree.ts

@@ -719,7 +719,7 @@ export const treeText = createDictionary({
       'Creating tree record {current:number|formatted}/{total:number|formatted}',
   },
   defaultTreeCreationLoadingMessage: {
-    'en-us': 'Default Tree Creation is in progress, please wait...'
+    'en-us': 'Default Tree Creation is in progress, please wait...',
   },
   missingRanks: {
     'en-us': 'Missing Ranks',

specifyweb/specify/management/commands/run_key_migration_functions.py

@@ -24,6 +24,7 @@
 from specifyweb.specify.migration_utils.misc_migrations import make_selectseries_false
 from specifyweb.specify.migration_utils.tectonic_ranks import create_default_tectonic_ranks, create_root_tectonic_node
 from specifyweb.backend.patches.migration_utils import apply_migrations as apply_patches
+from specifyweb.backend.setup_tool.schema_defaults import apply_schema_defaults
 
 logger = logging.getLogger(__name__)
 
@@ -48,6 +49,15 @@ def fix_cots(stdout: WriteToStdOut | None = None):
     log_and_run(funcs, stdout)
 
 def fix_schema_config(stdout: WriteToStdOut | None = None):
+    def apply_schema_overrides_for_all_disciplines(_apps):
+        Discipline = _apps.get_model('specify', 'Discipline')
+        for discipline in Discipline.objects.all():
+            if stdout is not None:
+                stdout(
+                    f"Applying schema defaults/overrides for discipline {discipline.id} ({discipline.type})..."
+                )
+            apply_schema_defaults(discipline)
+
     funcs = [
         # usc.update_all_table_schema_config_with_defaults,
         usc.create_geo_table_schema_config_with_defaults, # specify 0002
@@ -80,6 +90,7 @@ def fix_schema_config(stdout: WriteToStdOut | None = None):
         usc.componets_schema_config_migrations, # specify 0040
         usc.create_discipline_type_picklist, # specify 0042
         usc.update_discipline_type_splocalecontaineritem, # specify 0042
+        apply_schema_overrides_for_all_disciplines,
         usc.deduplicate_schema_config_orm,
     ]
     log_and_run(funcs, stdout)