Refactor TreeRankRecord to allow null tree id

specifyweb/frontend/js_src/lib/components/Interactions/InteractionDialog.tsx

@@ -204,23 +204,27 @@ export function InteractionDialog({
       })),
     });
 
-    const [collectionHasSeveralTypes] = useAsyncState(
-      React.useCallback(
-        async () =>
-          fetchDomain.then(async (schema) => Object.keys(schema.collectionObjectTypeCatalogNumberFormats).length > 1),
-        []
-      ),
-      false
-    );
+  const [collectionHasSeveralTypes] = useAsyncState(
+    React.useCallback(
+      async () =>
+        fetchDomain.then(
+          async (schema) =>
+            Object.keys(schema.collectionObjectTypeCatalogNumberFormats)
+              .length > 1
+        ),
+      []
+    ),
+    false
+  );
 
   function handleParse(): RA<string> | undefined {
     const parseResults = split(catalogNumbers).map((value) =>
       parseValue(parser, inputRef.current ?? undefined, value)
     );
 
     const errorMessages = parseResults
-    .filter((result): result is InvalidParseResult => !result.isValid)
-    .map(({ reason, value }) => `${reason} (${value})`);
+      .filter((result): result is InvalidParseResult => !result.isValid)
+      .map(({ reason, value }) => `${reason} (${value})`);
 
     if (errorMessages.length > 0 && collectionHasSeveralTypes === false) {
       setValidation(errorMessages);
@@ -233,10 +237,10 @@ export function InteractionDialog({
 
     if (collectionHasSeveralTypes === true) {
       const parsedCatNumber = split(catalogNumbers);
-    
+
       setCatalogNumbers(parsedCatNumber.join('\n'));
       setState({ type: 'MainState' });
-    
+
       return parsedCatNumber.map(String);
     }
 

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

@@ -1,5 +1,6 @@
 import type { IR, RA, RR } from '../../utils/types';
 import { group, removeKey, split, toLowerCase } from '../../utils/utils';
+import type { AnyTree } from '../DataModel/helperTypes';
 import type { SpecifyTable } from '../DataModel/specifyTable';
 import { strictGetTable } from '../DataModel/tables';
 import type { Tables } from '../DataModel/types';
@@ -47,8 +48,11 @@ const toTreeRecordRanks = (
     ])
   );
 
-const toTreeRecordVariety = (lines: RA<SplitMappingPath>): TreeRecord => {
-  const treeDefinitions = getTreeDefinitions('Taxon', 'all');
+const toTreeRecordVariety = (
+  tableName: AnyTree['tableName'],
+  lines: RA<SplitMappingPath>
+): TreeRecord => {
+  const treeDefinitions = getTreeDefinitions(tableName, 'all');
 
   return {
     ranks: Object.fromEntries(
@@ -87,7 +91,7 @@ const toTreeRecordVariety = (lines: RA<SplitMappingPath>): TreeRecord => {
               : formatTreeRankKey(rankName, treeName),
             {
               treeNodeCols: toTreeRecordRanks(mappedFields),
-              treeId,
+              treeId: treeDefinitions.length > 1 ? treeId : undefined,
             },
           ];
         });
@@ -166,7 +170,7 @@ const toUploadable = (
           mustMatchPreferences.includes(table.name)
             ? 'mustMatchTreeRecord'
             : 'treeRecord',
-          toTreeRecordVariety(lines),
+          toTreeRecordVariety(table.name, lines),
         ] as const,
       ])
     : Object.fromEntries([

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

@@ -1,4 +1,5 @@
 import type { IR, RA, RR } from '../../utils/types';
+import type { AnyTree } from '../DataModel/helperTypes';
 import type { SpecifyTable } from '../DataModel/specifyTable';
 import { strictGetTable } from '../DataModel/tables';
 import type { Tables } from '../DataModel/types';
@@ -80,16 +81,16 @@ const parseTree = (
         ...mappingPath,
         ...(typeof rankData === 'object' &&
         typeof rankData.treeId === 'number' &&
-        getTreeDefinitions('Taxon', 'all').length > 1
-          ? [resolveTreeId(rankData.treeId)]
+        getTreeDefinitions(table.name as 'Geography', 'all').length > 1
+          ? [resolveTreeId(table.name as 'Geography', rankData.treeId)]
           : []),
         formatTreeRank(getRankNameFromKey(rankName)),
       ]
     )
   );
 
-const resolveTreeId = (id: number): string => {
-  const treeDefinition = getTreeDefinitions('Taxon', id);
+const resolveTreeId = (tableName: AnyTree['tableName'], id: number): string => {
+  const treeDefinition = getTreeDefinitions(tableName, id);
   return formatTreeDefinition(treeDefinition[0].definition.name);
 };
 

specifyweb/frontend/js_src/lib/tests/fixtures/uploadplan.1.json

@@ -283,40 +283,34 @@
                             "default": null,
                             "column": "Class"
                           }
-                        },
-                        "treeId": 1
+                        }
                       },
                       "Family": {
                         "treeNodeCols": {
                           "name": "Family"
-                        },
-                        "treeId": 1
+                        }
                       },
                       "Genus": {
                         "treeNodeCols": {
                           "name": "Genus"
-                        },
-                        "treeId": 1
+                        }
                       },
                       "Subgenus": {
                         "treeNodeCols": {
                           "name": "Subgenus"
-                        },
-                        "treeId": 1
+                        }
                       },
                       "Species": {
                         "treeNodeCols": {
                           "name": "Species",
                           "author": "Species Author"
-                        },
-                        "treeId": 1
+                        }
                       },
                       "Subspecies": {
                         "treeNodeCols": {
                           "name": "Subspecies",
                           "author": "Subspecies Author"
-                        },
-                        "treeId": 1
+                        }
                       }
                     }
                   }

specifyweb/specify/tree_utils.py

@@ -1,7 +1,8 @@
 from typing import Tuple, List
 from django.db.models import Q, Count, Model
+
 import specifyweb.specify.models as spmodels
-from specifyweb.specify.datamodel import datamodel
+from specifyweb.specify.datamodel import datamodel, Table
 
 lookup = lambda tree: (tree.lower() + 'treedef')
 
@@ -48,3 +49,39 @@ def get_treedefs(collection: spmodels.Collection, tree_name: str) ->  List[Tuple
 
     return result
 
+def get_default_treedef(table: Table, collection):
+    if table.name.lower() not in SPECIFY_TREES:
+        raise Exception(f"unexpected tree type: {table.name}")
+
+    if table.name == 'Taxon':
+        return collection.discipline.taxontreedef
+
+    elif table.name == "Geography":
+        return collection.discipline.geographytreedef
+
+    elif table.name == "LithoStrat":
+        return collection.discipline.lithostrattreedef
+
+    elif table.name == "GeologicTimePeriod":
+        return collection.discipline.geologictimeperiodtreedef
+
+    elif table.name == "Storage":
+        return collection.discipline.division.institution.storagetreedef
+
+    elif table.name == 'TectonicUnit':
+        return collection.discipline.tectonicunittreedef
+
+    return None
+
+def get_treedefitem_model(tree: str):
+    return getattr(spmodels, tree.lower().title() + 'treedefitem')
+
+def get_treedef_model(tree: str):
+    return getattr(spmodels, tree.lower().title() + 'treedef')
+
+def get_models(name: str):
+    tree_def_model = get_treedef_model(name)
+    tree_rank_model = get_treedefitem_model(name)
+    tree_node_model = getattr(spmodels, name.lower().title())
+
+    return tree_def_model, tree_rank_model, tree_node_model

specifyweb/workbench/upload/scoping.py

@@ -5,6 +5,7 @@
 from specifyweb.specify.func import CustomRepr
 from specifyweb.specify.load_datamodel import DoesNotExistError
 from specifyweb.specify import models
+from specifyweb.specify.tree_utils import get_default_treedef
 from specifyweb.specify.uiformatters import get_uiformatter, get_catalognumber_format, UIFormatter
 from specifyweb.specify.utils import get_picklists
 from specifyweb.stored_queries.format import get_date_format
@@ -347,37 +348,15 @@ def set_order_number(
 def apply_scoping_to_treerecord(tr: TreeRecord, collection) -> ScopedTreeRecord:
     table = datamodel.get_table_strict(tr.name)
 
-    treedef = None
-    if table.name == 'Taxon':
-        if treedef is None:
-            treedef = collection.discipline.taxontreedef
-
-    elif table.name == "Geography":
-        treedef = collection.discipline.geographytreedef
-
-    elif table.name == "LithoStrat":
-        treedef = collection.discipline.lithostrattreedef
-
-    elif table.name == "GeologicTimePeriod":
-        treedef = collection.discipline.geologictimeperiodtreedef
-
-    elif table.name == "Storage":
-        treedef = collection.discipline.division.institution.storagetreedef
-
-    elif table.name == 'TectonicUnit':
-        treedef = collection.discipline.tectonicunittreedef
-
-    else:
-        raise Exception(f"unexpected tree type: {table.name}")
-
+    treedef = get_default_treedef(table, collection)
     if treedef is None:
         raise ValueError(f"Could not find treedef for table {table.name}")
 
     treedefitems = list(treedef.treedefitems.order_by('rankid'))
     treedef_ranks = [tdi.name for tdi in treedefitems]
     for rank in tr.ranks:
         is_valid_rank = (hasattr(rank, 'rank_name') and rank.rank_name in treedef_ranks) or (rank in treedef_ranks) # type: ignore
-        if not is_valid_rank and isinstance(rank, TreeRankRecord) and not rank.check_rank(table.name):
+        if not is_valid_rank and (isinstance(rank, TreeRankRecord) and not rank.validate_rank(tr.name)):
             raise Exception(f'"{rank}" not among {table.name} tree ranks: {treedef_ranks}')
 
     root = list(
@@ -392,6 +371,7 @@ def apply_scoping_to_treerecord(tr: TreeRecord, collection) -> ScopedTreeRecord:
                 r, table.name, treedef.id if treedef else None
             ).tree_rank_record()
             if isinstance(r, str)
+            else r._replace(treedef_id=treedef.id) if r.treedef_id is None  # Adjust treeid for parsed JSON plans
             else r
         ): {
             f: extend_columnoptions(colopts, collection, table.name, f)
@@ -400,6 +380,8 @@ def apply_scoping_to_treerecord(tr: TreeRecord, collection) -> ScopedTreeRecord:
         for r, cols in tr.ranks.items()
     }
 
+    scoped_cotypes = models.Collectionobjecttype.objects.filter(collection=collection)
+
     return ScopedTreeRecord(
         name=tr.name,
         ranks=scoped_ranks,
@@ -408,4 +390,5 @@ def apply_scoping_to_treerecord(tr: TreeRecord, collection) -> ScopedTreeRecord:
         root=root[0] if root else None,
         disambiguation={},
         batch_edit_pack=None,
+        scoped_cotypes=scoped_cotypes
     )