Merge pull request #5091 from specify/issue-4980

Add a feature to choose type of taxon tree in WB

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

@@ -24,5 +24,6 @@ test('domain data is fetched and parsed correctly', async () =>
     ],
     paleoContextChildTable: 'collectionobject',
     referenceSymbol: '#',
-    treeSymbol: '$',
+    treeRankSymbol: '$',
+    treeDefinitionSymbol: '%',
   }));

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

@@ -29,7 +29,8 @@ type Schema = {
     'Institution'
   ];
   readonly referenceSymbol: string;
-  readonly treeSymbol: string;
+  readonly treeDefinitionSymbol: string;
+  readonly treeRankSymbol: string;
   readonly fieldPartSeparator: string;
 };
 
@@ -60,8 +61,10 @@ const schemaBase: Writable<Schema> = {
 
   // Prefix for -to-many indexes
   referenceSymbol: '#',
+  // Prefix for Tree Definitions
+  treeDefinitionSymbol: '%',
   // Prefix for tree ranks
-  treeSymbol: '$',
+  treeRankSymbol: '$',
   // Separator for partial fields (date parts in Query Builder)
   fieldPartSeparator: '-',
 };

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

@@ -118,11 +118,14 @@ export function getTreeDefinitions<TREE_NAME extends AnyTree['tableName']>(
     tableName
   );
 
-  return typeof treeDefinitionId === 'number'
-    ? specificTreeDefinitions.filter(
-        ({ definition }) => definition.id === treeDefinitionId
-      )
-    : specificTreeDefinitions;
+  if (typeof treeDefinitionId === 'number') {
+    const resolvedDefinition = specificTreeDefinitions.find(
+      ({ definition }) => definition.id === treeDefinitionId
+    );
+    return resolvedDefinition === undefined
+      ? specificTreeDefinitions
+      : [resolvedDefinition];
+  } else return specificTreeDefinitions;
 }
 
 export function getTreeDefinitionItems<TREE_NAME extends AnyTree['tableName']>(

specifyweb/frontend/js_src/lib/components/Syncer/__tests__/index.test.ts

@@ -94,8 +94,8 @@ test('Editing Data Object Formatter', () => {
         </switch>
       </format>
       <aggregators>
-        <aggregator name='AccessionAgent' title='AccessionAgent' class='edu.ku.brc.specify.datamodel.Agent' default='true' separator='' ending='' format='AccessionAgent'/>
-        <aggregator name='AccessionAgent' title='AccessionAgent' class='edu.ku.brc.specify.datamodel.AccessionAgent' default='true' separator='' ending='' format='AccessionAgent'/>
+        <aggregator name='AccessionAgent' title='AccessionAgent' class='edu.ku.brc.specify.datamodel.Agent' default='true' separator='; ' ending='' format='AccessionAgent'/>
+        <aggregator name='AccessionAgent' title='AccessionAgent' class='edu.ku.brc.specify.datamodel.AccessionAgent' default='true' separator='; ' ending='' format='AccessionAgent'/>
       </aggregators>
     </formatters>"
   `);

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

@@ -37,7 +37,6 @@ export type HtmlGeneratorFieldData = {
   readonly isDefault?: boolean;
   readonly isRelationship?: boolean;
   readonly tableName?: keyof Tables;
-  readonly tableTreeDefName?: string;
 };
 
 type MappingLineBaseProps = {

specifyweb/frontend/js_src/lib/components/WbPlanView/__tests__/mappingHelpers.test.ts

@@ -16,16 +16,16 @@ theories(valueIsToManyIndex, [
   [[`${schema.referenceSymbol}2`], true],
   [[`${schema.referenceSymbol}999`], true],
   [['collectionobject'], false],
-  [[`${schema.treeSymbol}Kingdom`], false],
+  [[`${schema.treeRankSymbol}Kingdom`], false],
 ]);
 
 theories(valueIsTreeRank, [
   [[`${schema.referenceSymbol}1`], false],
   [[`${schema.referenceSymbol}2`], false],
   [[`${schema.referenceSymbol}999`], false],
   [['collectionobject'], false],
-  [[`${schema.treeSymbol}Kingdom`], true],
-  [[`${schema.treeSymbol}County`], true],
+  [[`${schema.treeRankSymbol}Kingdom`], true],
+  [[`${schema.treeRankSymbol}County`], true],
 ]);
 
 theories(getNumberFromToManyIndex, [
@@ -36,8 +36,8 @@ theories(getNumberFromToManyIndex, [
 ]);
 
 theories(getNameFromTreeRankName, [
-  [[`${schema.treeSymbol}Kingdom`], 'Kingdom'],
-  [[`${schema.treeSymbol}County`], 'County'],
+  [[`${schema.treeRankSymbol}Kingdom`], 'Kingdom'],
+  [[`${schema.treeRankSymbol}County`], 'County'],
 ]);
 
 theories(findDuplicateMappings, [

specifyweb/frontend/js_src/lib/components/WbPlanView/__tests__/navigator.test.ts

@@ -314,70 +314,60 @@ theories(getMappingLineData, [
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Phylum: {
             optionLabel: 'Phylum',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Class: {
             optionLabel: 'Class',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Order: {
             optionLabel: 'Order',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Family: {
             optionLabel: 'Family',
             isRelationship: true,
             isDefault: true,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subfamily: {
             optionLabel: 'Subfamily',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Genus: {
             optionLabel: 'Genus',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subgenus: {
             optionLabel: 'Subgenus',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Species: {
             optionLabel: 'Species',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subspecies: {
             optionLabel: 'Subspecies',
             isRelationship: true,
             isDefault: false,
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
         },
         tableName: 'Taxon',
@@ -870,70 +860,60 @@ theories(getMappingLineData, [
             isRelationship: true,
             optionLabel: 'Class',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Family: {
             isDefault: true,
             isRelationship: true,
             optionLabel: 'Family',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Genus: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Genus',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Kingdom: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Kingdom',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Order: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Order',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Phylum: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Phylum',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Species: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Species',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subfamily: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Subfamily',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subgenus: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Subgenus',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
           $Subspecies: {
             isDefault: false,
             isRelationship: true,
             optionLabel: 'Subspecies',
             tableName: 'Taxon',
-            tableTreeDefName: 'Taxonomy',
           },
         },
         selectLabel: localized('Taxon'),

specifyweb/frontend/js_src/lib/components/WbPlanView/mappingHelpers.ts

@@ -29,9 +29,20 @@ export const valueIsToManyIndex = (value: string | undefined): boolean =>
   value?.slice(0, schema.referenceSymbol.length) === schema.referenceSymbol ||
   false;
 
+/**
+ * Returns whether a value is any special tree-related meta information
+ * (e.g. tree defintiion, tree rank)
+ */
+export const valueIsTreeMeta = (value: string | undefined): boolean =>
+  valueIsTreeDefinition(value) || valueIsTreeRank(value);
+
+/** Returns whether a value is a tree definition name (e.x %Taxonomy) */
+export const valueIsTreeDefinition = (value: string | undefined): boolean =>
+  value?.startsWith(schema.treeDefinitionSymbol) ?? false;
+
 /** Returns whether a value is a tree rank name (e.x $Kingdom, $Order) */
 export const valueIsTreeRank = (value: string | undefined): boolean =>
-  value?.startsWith(schema.treeSymbol) || false;
+  value?.startsWith(schema.treeRankSymbol) ?? false;
 
 /**
  * Returns index from a formatted -to-many index value (e.x #1 => 1)
@@ -40,6 +51,14 @@ export const valueIsTreeRank = (value: string | undefined): boolean =>
 export const getNumberFromToManyIndex = (value: string): number =>
   Number(value.slice(schema.referenceSymbol.length));
 
+/**
+ * Returns tree definition name from a complete tree definition name
+ * (e.x %Taxonomy => Taxonomy)
+ * Opposite of formatTreeDefinition
+ */
+export const getNameFromTreeDefinitionName = (value: string): string =>
+  value.slice(schema.treeDefinitionSymbol.length);
+
 /*
  * BUG: in places where output of this function is displayed to the user,
  *   make sure to use tree rank title instead of name
@@ -51,7 +70,7 @@ export const getNumberFromToManyIndex = (value: string): number =>
  *
  */
 export const getNameFromTreeRankName = (value: string): string =>
-  value.slice(schema.treeSymbol.length);
+  value.slice(schema.treeRankSymbol.length);
 
 /**
  * Returns a formatted -to-many index from an index (e.x 1 => #1)
@@ -61,7 +80,7 @@ export const formatToManyIndex = (index: number): string =>
   `${schema.referenceSymbol}${index}`;
 
 // Meta fields
-export const anyTreeRank = `${schema.fieldPartSeparator}any`;
+export const anyTreeRank = `${schema.fieldPartSeparator}any` as const;
 export const formattedEntry = `${schema.fieldPartSeparator}formatted`;
 
 /**
@@ -75,14 +94,22 @@ export const formattedEntry = `${schema.fieldPartSeparator}formatted`;
  */
 export const emptyMapping = '0';
 
+/**
+ * Returns a complete tree definition name from a tree definition name
+ * (e.x Taxononomy => %Taxonomy)
+ * Opposite of getNameFromTreeDefinitionName
+ */
+export const formatTreeDefinition = (definitionName: string): string =>
+  `${schema.treeDefinitionSymbol}${definitionName}`;
+
 /**
  * Returns a complete tree rank name from a tree rank name
  * (e.x Kingdom => $Kingdom)
  * Opposite of getNameFromTreeRankName
  *
  */
 export const formatTreeRank = (rankName: string): string =>
-  `${schema.treeSymbol}${rankName}`;
+  `${schema.treeRankSymbol}${rankName}`;
 
 // Match fields names like startDate_fullDate, but not _formatted
 export const valueIsPartialField = (value: string): boolean =>
@@ -160,7 +187,7 @@ export const getGenericMappingPath = (mappingPath: MappingPath): MappingPath =>
   mappingPath.filter(
     (mappingPathPart) =>
       !valueIsToManyIndex(mappingPathPart) &&
-      !valueIsTreeRank(mappingPathPart) &&
+      !valueIsTreeMeta(mappingPathPart) &&
       mappingPathPart !== formattedEntry &&
       mappingPathPart !== emptyMapping
   );

specifyweb/frontend/js_src/lib/components/WbPlanView/mappingPreview.ts

@@ -22,6 +22,7 @@ import {
   parsePartialField,
   valueIsPartialField,
   valueIsToManyIndex,
+  valueIsTreeDefinition,
   valueIsTreeRank,
 } from './mappingHelpers';
 import { getMappingLineData } from './navigator';
@@ -120,16 +121,19 @@ export function generateMappingPathPreview(
     : 1;
   const toManyIndexFormatted = toManyIndexNumber > 1 ? toManyIndex : undefined;
 
-  const [databaseFieldName, databaseTableOrRankName, databaseParentTableName] =
-    mappingPathSubset([baseTableName, ...mappingPath]);
+  const [
+    databaseFieldName,
+    databaseTableOrRankName,
+    databaseParentTableOrTreeName,
+  ] = mappingPathSubset([baseTableName, ...mappingPath]);
 
   // Attributes parts of filedLables to each variable or creates one if empty
   const [
     fieldName = camelToHuman(databaseFieldName),
     tableOrRankName = camelToHuman(
       getNameFromTreeRankName(databaseTableOrRankName)
     ),
-    parentTableName = camelToHuman(databaseParentTableName),
+    parentTableOrTreeName = camelToHuman(databaseParentTableOrTreeName),
   ] = mappingPathSubset(fieldLabels);
 
   const isAnyRank = databaseTableOrRankName === formatTreeRank(anyTreeRank);
@@ -163,16 +167,20 @@ export function generateMappingPathPreview(
   const tableNameFormatted =
     tablesToHide.has(databaseTableOrRankName) &&
     databaseFieldName !== formattedEntry
-      ? [parentTableName || tableNameNonEmpty]
+      ? [parentTableOrTreeName || tableNameNonEmpty]
       : genericTables.has(databaseTableOrRankName)
-      ? [parentTableName, tableNameNonEmpty]
+      ? [parentTableOrTreeName, tableNameNonEmpty]
       : [tableNameNonEmpty];
 
   return filterArray([
     ...(valueIsTreeRank(databaseTableOrRankName)
-      ? [isAnyRank ? parentTableName : tableOrRankName]
+      ? [isAnyRank ? parentTableOrTreeName : tableOrRankName]
       : tableNameFormatted),
     fieldNameFormatted,
+    ...(valueIsTreeRank(databaseTableOrRankName) &&
+    valueIsTreeDefinition(databaseParentTableOrTreeName)
+      ? [parentTableOrTreeName]
+      : []),
     toManyIndexFormatted,
   ])
     .filter(Boolean)